Mock Version: 1.1.18 Mock Version: 1.1.18 ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target ppc64 --nodeps builddir/build/SPECS/gromacs.spec'], False, '/var/lib/mock/dist-6E-epel-build-1494340-250476/root/', None, 86400, True, False, 419, 492, None, False, None, logger=) Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target ppc64 --nodeps builddir/build/SPECS/gromacs.spec'] warning: Could not canonicalize hostname: ppc12.phx2.fedoraproject.org Building target platforms: ppc64 Building for target ppc64 Wrote: /builddir/build/SRPMS/gromacs-4.5.5-2.el6.src.rpm Child returncode was: 0 LEAVE do --> ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target ppc64 --nodeps builddir/build/SPECS/gromacs.spec'], False, '/var/lib/mock/dist-6E-epel-build-1494340-250476/root/', None, 86400, True, False, 419, 492, None, False, None, logger=) Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target ppc64 --nodeps builddir/build/SPECS/gromacs.spec'] Building target platforms: ppc64 Building for target ppc64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.uTbuRt + umask 022 + cd /builddir/build/BUILD + LANG=C + export LANG + unset DISPLAY + cd /builddir/build/BUILD + rm -rf gromacs-4.5.5 + /usr/bin/gzip -dc /builddir/build/SOURCES/gromacs-4.5.5.tar.gz + /bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd gromacs-4.5.5 + /bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (gromacs-GMXRC.patch):' Patch #0 (gromacs-GMXRC.patch): + /bin/cat /builddir/build/SOURCES/gromacs-GMXRC.patch + /usr/bin/patch -s -p1 -b --suffix .gmxrc --fuzz=0 + echo 'Patch #1 (gromacs-gmxdemo.patch):' Patch #1 (gromacs-gmxdemo.patch): + /bin/cat /builddir/build/SOURCES/gromacs-gmxdemo.patch + /usr/bin/patch -s -p1 -b --suffix .gmxdemo --fuzz=0 + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.EuIJcT + umask 022 + cd /builddir/build/BUILD + cd gromacs-4.5.5 + LANG=C + export LANG + unset DISPLAY + export 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC' + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC' + export 'LIBS=-L/usr/lib64/atlas -lblas -llapack' + LIBS='-L/usr/lib64/atlas -lblas -llapack' + export 'DEFOPTS=-D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=lib64' + DEFOPTS='-D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=lib64' + export 'SINGLE=-D GMX_DOUBLE=OFF' + SINGLE='-D GMX_DOUBLE=OFF' + export 'DOUBLE=-D GMX_DOUBLE=ON' + DOUBLE='-D GMX_DOUBLE=ON' + export 'MPI=-D GMX_MPI=ON' + MPI='-D GMX_MPI=ON' + export 'NOASM=-D GMX_ACCELERATION=OFF' + NOASM='-D GMX_ACCELERATION=OFF' + mkdir single + cd single + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export FFLAGS + /usr/bin/cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DCMAKE_SKIP_RPATH:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=ON -D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=lib64 -D GMX_DOUBLE=OFF .. -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Failed -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Failed -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for include files HAVE_STRING_H -- Looking for include files HAVE_STRING_H - found -- Looking for include files HAVE_MATH_H -- Looking for include files HAVE_MATH_H - found -- Looking for include files HAVE_LIMITS_H -- Looking for include files HAVE_LIMITS_H - found -- Looking for include files HAVE_MEMORY_H -- Looking for include files HAVE_MEMORY_H - found -- Looking for include files HAVE_UNISTD_H -- Looking for include files HAVE_UNISTD_H - found -- Looking for include files HAVE_DIRECT_H -- Looking for include files HAVE_DIRECT_H - not found. -- Looking for include files HAVE_PWD_H -- Looking for include files HAVE_PWD_H - found -- Looking for include files HAVE_STDINT_H -- Looking for include files HAVE_STDINT_H - found -- Looking for include files HAVE_STDLIB_H -- Looking for include files HAVE_STDLIB_H - found -- Looking for include files HAVE_PTHREAD_H -- Looking for include files HAVE_PTHREAD_H - found -- Looking for include files HAVE_DIRENT_H -- Looking for include files HAVE_DIRENT_H - found -- Looking for include files HAVE_INTTYPES_H -- Looking for include files HAVE_INTTYPES_H - found -- Looking for include files HAVE_REGEX_H -- Looking for include files HAVE_REGEX_H - found -- Looking for include files HAVE_SYS_TYPES_H -- Looking for include files HAVE_SYS_TYPES_H - found -- Looking for include files HAVE_SYS_STAT_H -- Looking for include files HAVE_SYS_STAT_H - found -- Looking for include files HAVE_SYS_TIME_H -- Looking for include files HAVE_SYS_TIME_H - found -- Looking for include files HAVE_RPC_RPC_H -- Looking for include files HAVE_RPC_RPC_H - found -- Looking for include files HAVE_RPC_XDR_H -- Looking for include files HAVE_RPC_XDR_H - found -- Looking for include files HAVE_XMMINTRIN_H -- Looking for include files HAVE_XMMINTRIN_H - not found. -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - not found. -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include files HAVE_PMMINTRIN_H - not found. -- Looking for include files HAVE_SMMINTRIN_H -- Looking for include files HAVE_SMMINTRIN_H - not found. -- Looking for include files HAVE_IO_H -- Looking for include files HAVE_IO_H - not found. -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strdup -- Looking for strdup - found -- Looking for vprintf -- Looking for vprintf - found -- Looking for memcmp -- Looking for memcmp - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Looking for _aligned_malloc -- Looking for _aligned_malloc - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for isnan -- Looking for isnan - found -- Looking for _isnan -- Looking for _isnan - not found -- Looking for isfinite -- Looking for isfinite - not found -- Looking for _isfinite -- Looking for _isfinite - not found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for cbrt in m -- Looking for cbrt in m - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of bool -- Check size of bool - failed -- Check size of int -- Check size of int - done -- Check size of long int -- Check size of long int - done -- Check size of long long int -- Check size of long long int - done -- Check size of off_t -- Check size of off_t - done -- Check size of void * -- Check size of void * - done -- Check size of uid_t -- Check size of uid_t - done -- Check size of gid_t -- Check size of gid_t - done -- Check size of size_t -- Check size of size_t - done -- Check size of off_t -- Check size of off_t - done -- Check if the system is big endian -- Searching 16 bit integer -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - big endian -- checking for module 'libxml-2.0' -- found libxml-2.0, version 2.7.6 -- Found LibXml2: /usr/lib64/libxml2.so -- Looking for include files CMAKE_HAVE_PTHREAD_H -- Looking for include files CMAKE_HAVE_PTHREAD_H - found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Looking for include files HAVE_SCHED_H -- Looking for include files HAVE_SCHED_H - found -- Looking for sysconf -- Looking for sysconf - found -- Atomics found -- Setting build user & time -- Setting build user & time - OK -- Checking floating point format -- Checking floating point format - unknown -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for return type of signals -- Checking for return type of signals - void -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for inline keyword -- Checking for inline keyword - inline -- Checking for inline keyword -- Checking for inline keyword - inline -- Checking for pipe support -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Checking for MSVC x86 inline asm -- Checking for MSVC x86 inline asm - not supported -- Checking for system XDR support -- Checking for system XDR support - present -- Found FFTW3F: /usr/lib64/libfftw3f.so -- Found assembler: /usr/bin/as -- Loaded CMakeASM-ATTInformation - ASM-ATT support is still experimental, please report issues -- Configuring done -- Generating done -- Build files have been written to: /builddir/build/BUILD/gromacs-4.5.5/single + make VERBOSE=1 -j4 /usr/bin/cmake -H/builddir/build/BUILD/gromacs-4.5.5 -B/builddir/build/BUILD/gromacs-4.5.5/single --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles/progress.make make -f CMakeFiles/Makefile2 all make[1]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib/CMakeFiles/gmx.dir/depend.internal". Scanning dependencies of target gmx make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 0%] [ 0%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/princ.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/princ.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_fatal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_fatal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_fatal.c [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/topsort.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/topsort.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c Building C object src/gmxlib/CMakeFiles/gmx.dir/random.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/random.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c: In function 'gmx_sort_ilist_fe': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c:185: warning: unused variable 'bPert' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c: In function 'maxwell_speed': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c:93: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c:92: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_fatal.c:150: warning: 'bputi' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c:48: warning: 'm_op' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c:249: warning: 'dump_shit' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/checkpoint.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/checkpoint.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/dihres.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/dihres.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_real': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:448: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_ints': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:459: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_doubles': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:526: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_rvecs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:591: warning: unused variable 'n3' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpt_header': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:700: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 1 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpt_files': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1043: warning: unused variable 'j' [ 1%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'write_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1159: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1154: warning: unused variable 'flag_64bit' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'read_checkpoint': [ 1%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1459: warning: unused variable 'filename' Building C object src/gmxlib/CMakeFiles/gmx.dir/warninp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/warninp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/warninp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'list_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2001: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2001: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2000: warning: unused variable 'indent' Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_cyclecounter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_cyclecounter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_cyclecounter.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:429: warning: 'do_cpte_reals' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c: In function 'ta_dihres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c:78: warning: unused variable 'dp2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c:77: warning: unused variable 'typep' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sfactor.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sfactor.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sfactor.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ifunc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ifunc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ifunc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used [ 1%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/ffscanf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ffscanf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ffscanf.c /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_system_xdr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_system_xdr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_system_xdr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 1%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/macros.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/macros.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/macros.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/shift_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/shift_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 2 [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/atomprop.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/atomprop.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c: In function 'shift_LRcorrection': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:271: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:267: warning: unused variable 'qtot' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:266: warning: unused variable 'isp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:384: warning: 'rgbset' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c: In function 'gmx_atomprop_init': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c:246: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrnb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrnb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrnb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/tpxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/tpxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_pullgrp': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:212: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_iparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:931: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ilist':[ 2%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1179: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1200: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ilists': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1262: warning: unused variable 'bDum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1261: warning: unused variable 'renum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1261: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_grps': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1382: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1498: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1498: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_atomtypes': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1525: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_moltype': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1678: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_molblock': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1706: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_mtop': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1834: warning: unused variable 'i' Building C object src/gmxlib/CMakeFiles/gmx.dir/calch.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2046: warning: unused variable 'i' cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/calch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'read_tpx_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2347: warning: unused variable 'ltop' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'read_tps_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2376: warning: unused variable 'topconv' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c: In function 'gen_waterhydrogen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c:82: warning: unused variable 'kkk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/wman.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/wman.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'mydate': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:202: warning: unused variable 'num' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'print_tty_formatted': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:551: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_wikiman': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:672: warning: unused variable 'tmp2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:671: warning: unused variable 'link' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_htmlman': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:723: warning: unused variable 'link' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_py': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:966: warning: unused variable 'bHidden' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/string2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/string2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c: In function 'ltrim': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c:137: warning: unused variable 'tr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/matio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/matio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c: In function 'write_xpm_map_split': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'fac' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:661: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pargs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pargs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c: In function 'print_pargs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'buf2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 3 [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_asc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_asc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_asc.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/index.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/index.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'analyse_prot': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:365: warning: unused variable 'nnpres' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'gmx_residuetype_add': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:514: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'gmx_residuetype_init': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:546: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:545: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'analyse': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:734: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:732: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xtcio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xtcio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xtcio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pdbio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pdbio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: In function 'gmx_conect_add': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:681: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: In function 'read_pdbfile': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:705: warning: unused variable 'chidmax' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:704: warning: unused variable 'nres_ter_prev' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/readinp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/readinp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: In function 'get_einp': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c:283: warning: unused variable 'warn_buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: In function 'get_eenum': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c:456: warning: unused variable 'dum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 3%] [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/main.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/main.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c Building C object src/gmxlib/CMakeFiles/gmx.dir/orires.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/orires.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c: In function 'init_orires': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c:58: warning: unused variable 'nr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'par_fn': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:140: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'gmx_log_open': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:259: warning: unused variable 'testlen' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'init_multisystem': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:485: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'init_par': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:522: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:377: warning: 'comm_args' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 4 [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/calcgrid.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/calcgrid.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sortwater.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sortwater.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sortwater.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c: In function 'calc_grid': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c:98: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'set_default_time_unit': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:255: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'set_default_xvg_format': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:287: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:286: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'parse_common_args': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:578: warning: unused variable 'envstr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:577: warning: unused variable 'newdesc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:577: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:536: warning: unused variable 'npri_pa' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:529: warning: unused variable 'mantp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:409: warning: 'pdesc' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pbc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pbc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'low_set_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:285: warning: unused variable 'bXY' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'put_atom_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1195: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'put_atoms_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1209: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1209: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trnio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trnio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trnio.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_remove': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:339: warning: unused variable 'prev' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_open': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:438: warning: unused variable 'xdrid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:435: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_fopen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:640: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_fclose': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:654: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_int_get_file_position': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:783: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_get_output_file_positions': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:858: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:837: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:835: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:834: warning: unused variable 'pos_lo' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:834: warning: unused variable 'pos_hi' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:833: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:833: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_int_fsync': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:1005: warning: unused variable 'filen' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/maths.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/maths.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 4%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/mtxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mtxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: In function 'gmx_mtxio_write': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c:92: warning: unused variable 'bRead' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: In function 'gmx_mtxio_read': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c:166: warning: unused variable 'bRead' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 5 [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xvgr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xvgr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/libxdrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/libxdrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/replace.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/replace.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/replace.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'xvgropen_type': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:287: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'fgets3': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:442: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'read_xvg_legend': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:546: warning: unused variable 'ptr1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:546: warning: unused variable 'ptr0' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'read_xvg_time': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:697: warning: unused variable 'tend' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr3dfcoord': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:820: warning: unused variable 'xdrid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xtc_get_next_frame_start': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1546: warning: unused variable 'inp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr_xtc_seek_time': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1693: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr_xtc_get_last_frame_number': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1882: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/viewit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/viewit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/viewit.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/strdb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/strdb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/strdb.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/enxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/enxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/splitter.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 6 cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/splitter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/filenm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/filenm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'do_enxnms': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:392: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'do_eheader': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:448: warning: unused variable 'tempfix_nr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:446: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'open_enx': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:723: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'get_enx_state': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:1071: warning: unused variable 'pcouplmu_nm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:375: warning: 'gen_units' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_force2': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:116: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: In function 'set_default_file_name': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c:216: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'mk_border': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:346: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_blocks': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:424: warning: unused variable 'bSHK' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:420: warning: unused variable 'last_shk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:419: warning: unused variable 'ai' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:419: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'merge_sid': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:662: warning: unused variable 'nChanged' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'gen_sblocks': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:760: warning: unused variable 'isid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'istart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'find_constraint_range_recursive': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:866: warning: unused variable 'nconstr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: In function 'add_suffix_to_output_names': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'pd_determine_constraints_range': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:890: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:890: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c:951: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'minidx' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'ihome' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'minhome' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:932: warning: unused variable 'ia' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nrd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nra' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nvsite_constr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'ftype' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'nodeid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'bstart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'send' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'sstart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'maxatom' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'atom' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'mj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: At top level:/builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:832: warning: 'block2blocka' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rmpbc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rmpbc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rmpbc.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/inputrec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/inputrec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/inputrec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rando.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rando.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rando.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 6%] [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/bondfree.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/trxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/vmddlopen.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmddlopen.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/txtdump.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/txtdump.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'FENE_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:242: warning: unused variable 'dr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'do_1_thole': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:652: warning: unused variable 'r12n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c: In function 'choose_ff': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c:441: warning: unused variable 'eFF' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'posres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1254: warning: unused variable 'ki' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'cmap_dihs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1642: warning: unused variable 'psi2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1641: warning: unused variable 'psi1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1637: warning: unused variable 'l4' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'bonded_tab': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2350: warning: unused variable 'f' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2350: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'tab_angles': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2475: warning: unused variable 'snt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_qm_opts': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:991: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_block_title': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1037: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_blocka_title': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1050: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_block': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1103: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_atom': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1225: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1260: warning: unused variable 'grpnr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_header': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1423: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1063: warning: 'low_pr_block' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 7 [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/writeps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/writeps.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxcpp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxcpp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: In function 'cpp_open_file': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c:188: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: In function 'cpp_close_file': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c:577: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_xdr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_xdr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_xdr.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_matrix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_matrix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sighandler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sighandler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sighandler.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: In function 'free_matrix': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c:63: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: In function 'multi_regression': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c:174: warning: unused variable 'niter' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_arpack.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_arpack.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_arpack.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/vmdio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c: In function 'load_vmd_library': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c:234: warning: unused variable 'filename' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 8 [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/names.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/names.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/names.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrjac.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrjac.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrjac.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/confio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/confio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: In function 'read_espresso_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:451: warning: unused variable 'npar' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:451: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: In function 'read_stx_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:1397: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:1392: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:880: warning: 'get_conf' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/do_fit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/do_fit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: In function 'calc_fit_R': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c:104: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: In function 'do_fit_ndim': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c:215: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/typedefs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/typedefs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_block': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:108: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_blocka': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:118: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_atom': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:131: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:183: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_state': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:533: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/symtab.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/symtab.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/symtab.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mvdata.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mvdata.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_atoms': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:169: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:187: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:327: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:349: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_inputrec': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:466: warning: unused variable 'bAlloc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_molblock': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:497: warning: unused variable 'bAlloc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:312: warning: 'bc_idef' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 9 [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sparsematrix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sparsematrix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sparsematrix.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gbutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gbutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gbutil.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mshift.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mshift.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: In function 'compact_graph': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c:249: warning: unused variable 'e' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: In function 'done_graph': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c:405: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/md5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/md5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/futil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/futil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c: In function 'ffopen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c:446: warning: unused variable 'bf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/tcontrol.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/tcontrol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tcontrol.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ewald_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ewald_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ewald_util.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/smalloc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/smalloc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 10 [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/oenv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/oenv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/oenv.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c: In function 'save_free_aligned': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c:356: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c:356: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/3dview.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used[ 10%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_sort.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_sort.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_sort.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c: In function 'reset_view': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c:281: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mtop_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_atomnr_to_molblock_ind': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:150: warning: unused variable 'atoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_atominfo_global': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:177: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_ilistloop_all_next': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:449: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_global_cgs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:503: warning: unused variable 'atoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gen_local_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:773: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:773: warning: unused variable 'ftype_dest' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 10%] [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrama.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrama.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c Building C object src/gmxlib/CMakeFiles/gmx.dir/wgms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/wgms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wgms.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rbin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rbin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rbin.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: In function 'get_dih2': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:182: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: In function 'init_rama': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:312: warning: unused variable 'ePBC' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:179: warning: 'get_dih2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 11 [ 11%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/chargegroup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/chargegroup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/chargegroup.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 11%] [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/network.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/network.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c Building C object src/gmxlib/CMakeFiles/gmx.dir/invblock.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/invblock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/invblock.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: In function 'gmx_setup': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:82: warning: unused variable 'flag' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:82: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:80: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: In function 'gmx_setup_nodecomm': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:262: warning: unused variable 'num' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:262: warning: unused variable 'mpi_hostname' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'ni' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'ng' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'hostnum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'resultlen' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'rank' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xdrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xdrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xdrd.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 11%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/disre.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/disre.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_bin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_bin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_bin.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_rw.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_rw.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_rw.c [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/cinvsqrtdata.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/cinvsqrtdata.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/cinvsqrtdata.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 12 [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/copyrite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/copyrite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: In function 'calc_disres_R_6': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'jt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'kj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'ki' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: In function 'ta_disres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:372: warning: unused variable 'jt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:372: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_random.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_random.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: In function 'cool_quote': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c:193: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: In function 'please_cite': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c:535: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c: In function 'gmx_rng_update': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c:217: warning: unused variable 'lastx' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selvalue.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selvalue.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selvalue.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_permute.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_same.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: In function 'init_output_permute': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c:192: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: In function 'evaluate_permute': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c:240: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selhelp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selhelp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selhelp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c: In function 'evaluate_same_str': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c:499: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 13 [ 12%] [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selelem.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selelem.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selelem.c Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/scanner.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/scanner.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/scanner.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used scanner.c:1396: warning: 'yyunput' defined but not used scanner.c:1438: warning: 'input' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/parsetree.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/parsetree.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_insolidangle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_insolidangle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_selelem_set_method': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:556: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_sel_init_comparison': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:652: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_sel_init_modifier': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:835: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: In function 'evaluate_insolidangle': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:476: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: In function 'store_surface_point': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:829: warning: unused variable 'bin' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:829: warning: unused variable 'pbin' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:213: warning: 'set_comg_insolidangle' declared 'static' but never defined /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/scanner_internal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/scanner_internal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/scanner_internal.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/symrec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/parser.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/parser.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parser.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/compiler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/compiler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c: In function 'add_symbol': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c:395: warning: unused variable 'len' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_distance.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_distance.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_distance.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c: In function 'analyze_static': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c:2004: warning: unused variable 'next' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c:2004: warning: unused variable 'child' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 14 [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/mempool.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/mempool.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/mempool.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/params.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/params.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c: In function 'parse_values_varnum_expr': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c:676: warning: unused variable 'expr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_compare.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_compare.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_compare.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_position.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_position.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_keywords.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_keywords.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_keywords.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selection.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selection.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selection.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_simple.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_simple.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 15 [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selmethod.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selmethod.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selmethod.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/evaluate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/evaluate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/evaluate.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_merge.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_merge.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/trajana.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c: In function 'init_merge': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c:182: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: In function 'gmx_ana_traj_free': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c:322: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: In function 'gmx_ana_init_selections': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c:1200: warning: unused variable 'bOk' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used [ 15%] /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/position.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/position.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/poscalc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: In function 'merge_to_base': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c:797: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: In function 'gmx_ana_poscalc_update': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c:1282: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/nbsearch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/nbsearch.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/displacement.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/displacement.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 16 [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/indexutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/indexutil.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 16%] [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/centerofmass.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: In function 'gmx_stats_dump_xy': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c:449: warning: unused variable 'ok' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: In function 'gmx_stats_make_histogram': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c:505: warning: unused variable 'ok' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c: In function 'gmx_calc_cog': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c:55: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statistics/histogram.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/histogram.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_generic_cg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_generic_cg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c: In function 'gmx_nb_generic_cg_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:83: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:62: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:61: warning: unused variable 'nri' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used[ 16%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nonbonded.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nonbonded.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: In function 'do_nonbonded': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:313: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:311: warning: unused variable 'bWater' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:309: warning: unused variable 'sz' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: In function 'do_listed_vdw_q': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:664: warning: unused variable 'tmplist' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:655: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_free_energy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_free_energy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 17 [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_generic.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_generic.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c: In function 'gmx_nb_free_energy_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:102: warning: unused variable 'H' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:102: warning: unused variable 'G' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:91: warning: unused variable 'rinvsix' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:88: warning: unused variable 'vcoul' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel230.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c: In function 'gmx_nb_generic_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:81: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:61: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:60: warning: unused variable 'nri' cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel230.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: In function 'nb_kernel230': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: In function 'nb_kernel230nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c:336: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel213.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel213.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel312.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel312.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: In function 'nb_kernel213': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: In function 'nb_kernel213nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c:424: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel101.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel101.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: In function 'nb_kernel312': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: In function 'nb_kernel312nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c:733: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel223.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel223.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: In function 'nb_kernel101': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: In function 'nb_kernel101nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c:368: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: In function 'nb_kernel223': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: In function 'nb_kernel223nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c:427: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel334.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel334.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 18 [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel210.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel210.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: In function 'nb_kernel334': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: In function 'nb_kernel334nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c:798: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: In function 'nb_kernel210': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: In function 'nb_kernel210nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c:304: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel112.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel112.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: In function 'nb_kernel112': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: In function 'nb_kernel112nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c:574: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel130.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel130.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In function 'nb_kernel200': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In function 'nb_kernel200nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:286: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: In function 'nb_kernel130': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: In function 'nb_kernel130nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c:334: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel211.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel211.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel214.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel214.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: In function 'nb_kernel211': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: In function 'nb_kernel211nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c:390: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: In function 'nb_kernel214': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c: In function 'setup_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c:113: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: In function 'nb_kernel214nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c:622: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel110.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel110.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: In function 'nb_kernel110': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: In function 'nb_kernel110nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c:302: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 19 [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel131.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel131.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel232.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel232.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: In function 'nb_kernel131': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: In function 'nb_kernel131nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c:418: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used [ 19%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not usedBuilding C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel303.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel303.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: In function 'nb_kernel232': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: In function 'nb_kernel232nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c:616: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: In function 'nb_kernel303': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: In function 'nb_kernel303nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel304.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel304.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel124.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel124.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: In function 'nb_kernel304': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: In function 'nb_kernel304nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c:715: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 19%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: In function 'nb_kernel124': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: In function 'nb_kernel124nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c:615: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel430.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel430.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c: In function 'nb_kernel430': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c:105: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel221.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel221.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: In function 'nb_kernel221': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: In function 'nb_kernel221nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c:392: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 20 [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel420.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel420.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c: In function 'nb_kernel420': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c:105: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 20%] [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel400.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel400.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel100.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel100.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c: In function 'nb_kernel400': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c:100: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel030.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel030.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: In function 'nb_kernel100': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: In function 'nb_kernel100nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c:284: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel132.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel132.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: In function 'nb_kernel030': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: In function 'nb_kernel030nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c:322: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: In function 'nb_kernel132': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: In function 'nb_kernel132nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c:606: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 20%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel302.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel302.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel233.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel233.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: In function 'nb_kernel302': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: In function 'nb_kernel233': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: In function 'nb_kernel302nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c:715: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: In function 'nb_kernel233nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c:456: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel320.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel320.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: In function 'nb_kernel320': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: In function 'nb_kernel320nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c:327: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 21 [ 21%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel123.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel123.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel204.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel204.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: In function 'nb_kernel123': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: In function 'nb_kernel123nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: In function 'nb_kernel204': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: In function 'nb_kernel204nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c:568: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c: In function 'setup_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c:114: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel313.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel313.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel314.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel314.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: In function 'nb_kernel313': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: In function 'nb_kernel313nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c:476: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: In function 'nb_kernel314': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: In function 'nb_kernel314nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c:770: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel333.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel333.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel311.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel311.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: In function 'nb_kernel333': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: In function 'nb_kernel333nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c:504: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: In function 'nb_kernel311': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: In function 'nb_kernel311nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c:443: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 22 [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel331.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel331.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: In function 'nb_kernel331': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: In function 'nb_kernel331nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c:460: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel113.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel113.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel121.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel121.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: In function 'nb_kernel113': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: In function 'nb_kernel113nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c:420: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 22%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel010.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: In function 'nb_kernel121': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c:84: warning: unused variable 'gbtabscale' cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel010.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: In function 'nb_kernel121nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c:388: warning: unused variable 'gbtabscale' [ 22%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel201.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel201.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: In function 'nb_kernel010': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c:85: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: In function 'nb_kernel010nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c:292: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: In function 'nb_kernel201': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: In function 'nb_kernel201nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c:372: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 22%] [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel330.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel330.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel102.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel102.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel020.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel020.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: In function 'nb_kernel330': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: In function 'nb_kernel330nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c:342: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: In function 'nb_kernel102': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: In function 'nb_kernel102nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c:558: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 23 /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel231.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel231.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: In function 'nb_kernel020': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: In function 'nb_kernel020nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c:294: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: In function 'nb_kernel231': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: In function 'nb_kernel231nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c:422: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 23%] [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel203.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel133.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel203.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel133.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: In function 'nb_kernel203': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: In function 'nb_kernel203nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c:372: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: In function 'nb_kernel133': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: In function 'nb_kernel133nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c:452: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel224.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel224.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel323.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel323.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: In function 'nb_kernel224': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: In function 'nb_kernel323': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: In function 'nb_kernel224nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c:625: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: In function 'nb_kernel323nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c:479: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: At top level:/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel103.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel103.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel322.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel322.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: In function 'nb_kernel103': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: In function 'nb_kernel103nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c:368: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: In function 'nb_kernel322': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: In function 'nb_kernel322nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c:735: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 24 [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel104.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel104.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel324.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel324.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: In function 'nb_kernel104': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: In function 'nb_kernel104nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c:558: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel410.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel410.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: In function 'nb_kernel324': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: In function 'nb_kernel324nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c:773: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c: In function 'nb_kernel410': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c:106: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel202.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel202.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel212.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel212.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel114.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel114.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: In function 'nb_kernel202': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: In function 'nb_kernel202nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c:568: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: In function 'nb_kernel212': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: In function 'nb_kernel212nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c:584: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: In function 'nb_kernel114': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: In function 'nb_kernel114nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c:612: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel222.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel222.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 25 [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel332.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel332.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 25%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: In function 'nb_kernel222': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: In function 'nb_kernel222nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c:586: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel300.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel300.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: In function 'nb_kernel332': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: In function 'nb_kernel332nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c:750: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_c.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_c.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: In function 'nb_kernel300': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: In function 'nb_kernel300nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c:305: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel301.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel301.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel134.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel134.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: In function 'nb_kernel301': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: In function 'nb_kernel301nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: In function 'nb_kernel134': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: In function 'nb_kernel134nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c:644: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel321.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel321.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel234.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel234.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: In function 'nb_kernel321': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: In function 'nb_kernel321nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c:445: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: In function 'nb_kernel234': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: In function 'nb_kernel234nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c:654: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel310.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel310.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: In function 'nb_kernel310': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: In function 'nb_kernel310nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c:325: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 26 [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel122.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel122.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel111.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel111.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: In function 'nb_kernel122': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: In function 'nb_kernel122nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c:576: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: At top level:/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 26%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel120.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel120.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: In function 'nb_kernel111': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: In function 'nb_kernel111nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c:386: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: In function 'nb_kernel120': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: In function 'nb_kernel120nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c:304: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 26%] [ 26%] [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/srot.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sger.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel220.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/srot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/srot.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel220.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sger.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sger.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dswap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dswap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dswap.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 27 [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sgemm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sgemm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sgemm.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: In function 'nb_kernel220': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: In function 'nb_kernel220nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c:306: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dasum.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dasum.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dasum.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 27%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/daxpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/daxpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/daxpy.c [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/idamax.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/idamax.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/idamax.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 27%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dger.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dger.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dger.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dscal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dscal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dscal.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrsm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrsm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrsm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 28 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 28%] [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ddot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ddot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ddot.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ssyr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ssyr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssyr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sscal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sscal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sscal.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 28%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsyr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsyr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsyr2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/isamax.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/isamax.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/isamax.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dgemv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dgemv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dgemv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsyr2k.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsyr2k.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsyr2k.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 29 [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dgemm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dgemm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dgemm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrmv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrmv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrmv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dcopy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dcopy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dcopy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sasum.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sasum.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sasum.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 29%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sgemv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sgemv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sgemv.c [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsymv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsymv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsymv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/scopy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/scopy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/scopy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 30 [ 30%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 30%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/saxpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/saxpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/saxpy.c [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sswap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sswap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sswap.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/drot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/drot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/drot.c [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sdot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sdot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sdot.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 30%] [ 30%] [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dnrm2.c.o cd 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ssymv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssymv.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ssyr2k.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ssyr2k.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssyr2k.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 31 [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strmv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strmv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strmv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/snrm2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/snrm2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/snrm2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 31%] [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strsm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strsm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strsm.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgelqf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgelqf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgelqf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstein.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstein.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstein.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlascl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlascl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlascl.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlagtf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlagtf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlagtf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 32 [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasdq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasdq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasdq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 32%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarf.c.o [ 32%] cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarf.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarnv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarnv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarnv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasv2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasv2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasv2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 32%] [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasr.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 32%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 33 [ 33%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slagts.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slagts.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slagts.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarft.c [ 33%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarft.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 33%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 33%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrbx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrbx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrbx.c [ 33%] [ 33%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaruv.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgeqrf.c.o [ 33%] cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgeqrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgeqrf.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaruv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaruv.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormlq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormlq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormlq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 34 [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorg2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorg2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorg2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 34%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasrt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasrt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasrt.c [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorgqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlamrg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlamrg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlamrg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 34%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 34%] [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd8.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd8.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd8.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slange.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormql.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slange.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slange.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormql.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormql.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd3.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 35 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 35%] [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq1.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetri.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetri.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasrt2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaswp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaswp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaswp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorm2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorm2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorm2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 35%] [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorglq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorglq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorglq.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorm2l.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorm2l.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorm2l.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 36 [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd0.c.o cd 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-I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd7.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd7.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 36%] [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq6.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorglq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq6.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorglq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorglq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaruv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaruv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaruv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 36%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 36%] [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaev2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 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/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd0.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slabrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slabrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slabrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 37 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 37%] [ 37%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sbdsqr.c.o cd 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slar1vx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slar1vx.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsqr.c: In function 'sbdsqr_': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsqr.c:61: warning: unused variable 'ftmp' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 37%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorgl2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o 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cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 37%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlacpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlacpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlacpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 37%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsterf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsterf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsterf.c 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetf2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetf2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 38%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgebd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgebd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgebd2.c [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasda.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasda.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasda.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgebrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgebrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgebrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsteqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsteqr.c.o -c 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-I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstegr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstegr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaebz.c 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssytd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssytd2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrvx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrvx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrvx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 40 [ 40%] 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object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaed6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaed6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaed6.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slartg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slartg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slartg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 40%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd4.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 40%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorgbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 41 [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorml2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall 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-I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssterf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssterf.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorgbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorgbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorgbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarnv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarnv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarnv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ilasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ilasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ilasrt2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgl2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgl2.c.o -c 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-I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorgqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorgqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaset.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaset.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaset.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasrt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasrt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasrt.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 42%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq4.c.o cd 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-I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlae2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlae2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsytrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsytrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsytrd.c /usr/bin/cmake -E cmake_progress_report 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dtrtri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dtrtri.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 43%] [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstebz.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaswp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaswp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaswp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 43%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarfg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarfg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarfg.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaev2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaev2.c.o -c 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object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slascl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slascl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slascl.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slapy2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slapy2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slapy2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dtrti2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dtrti2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dtrti2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slassq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slassq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slassq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq4.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 45 cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq4.c [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetf2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetf2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetf2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd7.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd7.c.o -c 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object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssytrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssytrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssytrd.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgelq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgelq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgelq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorm2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorm2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorm2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 46 [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlansy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlansy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlansy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasdq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasdq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasdq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlanst.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlanst.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlanst.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsytd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsytd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsytd2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 46%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd8.c.o [ 46%] cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd8.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd8.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 47 [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlatrd.c.o cd 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-I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetri.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarfb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarfb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarfb.c 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-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slatrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slatrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorml2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorml2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorml2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlabrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlabrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlabrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgeqr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgeqr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgeqr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 48 [ 48%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 48%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq3.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq1.c.o -c 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-I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaset.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaset.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 48%] [ 48%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slamrg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slamrg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slamrg.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/strti2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/strti2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/strti2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 49 [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgeqrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgeqrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgeqrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlartg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlartg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlartg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dbdsqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dbdsqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd2.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c: In function 'dbdsqr_': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c:61: warning: unused variable 'ftmp' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 49%] [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgebd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgebd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgebd2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasdt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasdt.c.o -c 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-mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgelq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgelq2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarfb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarfb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarfb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssyevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssyevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssyevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 50%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 51 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasrt2.c [ 51%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlar1vx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlar1vx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlar1vx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 51%] [ 51%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slagtf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slagtf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slagtf.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slas2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slas2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slas2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 51%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slansy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slansy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slansy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 51%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd3.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 51%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 51%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 52 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 52%] [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorg2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorg2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorg2r.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetrs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetrs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetrs.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 52%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlapy2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlapy2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlapy2.c [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dbdsdc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dbdsdc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsdc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 52%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd4.c.o [ 52%] cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd4.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/strtri.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/strtri.c.o -c 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-I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormlq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormlq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgesdd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgesdd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgesdd.c 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cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 54%] [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlassq.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slae2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slae2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slae2.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorm2l.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorm2l.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o cd 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--param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o 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-DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormtr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slanst.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slanst.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slanst.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgeqr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgelqf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 55%] [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/alltoall.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/p2p_protocol.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/alltoall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/alltoall.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/p2p_protocol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/p2p_protocol.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used/builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 56 [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/barrier.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/barrier.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/barrier.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/p2p_send_recv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/p2p_send_recv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/p2p_send_recv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 56%] [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/bcast.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/p2p_wait.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/p2p_wait.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/p2p_wait.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/bcast.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/bcast.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/collective.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/collective.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/collective.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 56%] [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/profile.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/profile.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/profile.c Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/comm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/comm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/comm.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/pthreads.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/pthreads.c:165: warning: 'tMPI_Set_affinity' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 57 [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/errhandler.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/reduce.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/reduce.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/reduce.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/event.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/event.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/event.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 57%] /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/reduce_fast.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/reduce_fast.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/reduce_fast.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/gather.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/gather.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/gather.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 57%] [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/group.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/group.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/group.c Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/scatter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/scatter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/scatter.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 58 /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_init.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/tmpi_init.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/tmpi_init.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/topology.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/topology.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/topology.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/list.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/list.c.o -c 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warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/lock.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC 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/builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 58%] [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/numa_malloc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/numa_malloc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/numa_malloc.c Building C object 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CMakeFiles/gmx.dir/thread_mpi/collective.c.o CMakeFiles/gmx.dir/thread_mpi/profile.c.o CMakeFiles/gmx.dir/thread_mpi/comm.c.o CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o CMakeFiles/gmx.dir/thread_mpi/reduce.c.o CMakeFiles/gmx.dir/thread_mpi/event.c.o CMakeFiles/gmx.dir/thread_mpi/reduce_fast.c.o CMakeFiles/gmx.dir/thread_mpi/gather.c.o CMakeFiles/gmx.dir/thread_mpi/scatter.c.o CMakeFiles/gmx.dir/thread_mpi/group.c.o CMakeFiles/gmx.dir/thread_mpi/tmpi_init.c.o CMakeFiles/gmx.dir/thread_mpi/topology.c.o CMakeFiles/gmx.dir/thread_mpi/list.c.o CMakeFiles/gmx.dir/thread_mpi/type.c.o CMakeFiles/gmx.dir/thread_mpi/lock.c.o CMakeFiles/gmx.dir/thread_mpi/numa_malloc.c.o CMakeFiles/gmx.dir/thread_mpi/once.c.o -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib && /usr/bin/cmake -E cmake_symlink_library libgmx.so.6 libgmx.so.6 libgmx.so make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E 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"/builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib/CMakeFiles/md.dir/depend.internal". Scanning dependencies of target md make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 59 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 59%] [ 59%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 59%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/mdlib/CMakeFiles/md.dir/mdatom.c.o Building C object src/mdlib/CMakeFiles/md.dir/sim_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/sim_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdatom.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_mkl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_mkl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_mkl.c [ 59%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall_sse2_single.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 59%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdebin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c: In function 'init_mdatoms': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:55: warning: unused variable 'ilist' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'nmol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'mb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'calc_virial': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:362: warning: unused variable 'virtest' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:361: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'finish_run': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1358: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'init_md': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1467: warning: unused variable 'mod' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1467: warning: unused variable 'tmpt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1466: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1466: warning: unused variable 'j' [ 59%] Building C object src/mdlib/CMakeFiles/md.dir/coupling.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/coupling.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'init_mdebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:544: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:136: warning: unused variable 'nh' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'upd_mdebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:650: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'print_ebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:929: warning: unused variable 'enxlambda_data' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:918: warning: unused variable 'nor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:918: warning: unused variable 'ndr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'NHC_trotter': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:62: warning: unused variable 'jmax' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'boxv_trotter': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:184: warning: unused variable 'Winvm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:183: warning: unused variable 'T' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'berendsen_pcoupl': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:446: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'trotter_update': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:660: warning: unused variable 'consk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:657: warning: unused variable 'dumvir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:657: warning: unused variable 'dumpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'nd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'kT' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'reft' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'qmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'bmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'dvdlcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'pcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'ecorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:651: warning: unused variable 'ntgrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:651: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'init_npt_vars': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:784: warning: unused variable 'dumvir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:784: warning: unused variable 'dumpres' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:783: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'dvdlcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'pcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'ecorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:780: warning: unused variable 'tcstat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:779: warning: unused variable 'gc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:779: warning: unused variable 'ntgrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'NPT_energy': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'Q' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'W' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'dbaro' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:998: warning: unused variable 'tau' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:998: warning: unused variable 'eta' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'ngtcall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'qmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'bmass' [ 59%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/qm_orca.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_orca.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c: In function 'read_orca_output': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c:263: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 59%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftw3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftw3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw3.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw3.c:44: warning: 'gmx_fft_threads_initialized' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 60 [ 60%] Building C object src/mdlib/CMakeFiles/md.dir/partdec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/partdec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 60%] Building C object src/mdlib/CMakeFiles/md.dir/iteratedconstraints.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/iteratedconstraints.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'gmx_tx': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:101: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:100: warning: unused variable 'flag' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'init_partdec_constraint': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:508: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'init_partdec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:563: warning: unused variable 'nodeid' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'create_vsitelist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:769: warning: unused variable 'minidx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'setup_parallel_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:831: warning: unused variable 'recvbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:831: warning: unused variable 'sendbuf' [ 60%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:765: warning: 'create_vsitelist' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftw2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftw2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 60%] [ 60%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_double.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_sse2_double.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_sse2_double.c Building C object src/mdlib/CMakeFiles/md.dir/vsite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/vsite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c: In function 'done_iterating': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c:103: warning: unused variable 'xmin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 60%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/qmmm.c.o /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qmmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 60%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'constr_vsiten': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:376: warning: unused variable 'xs' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'construct_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'rtmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'vtmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'reftmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:417: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite2': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:588: warning: unused variable 'b' Building C object src/mdlib/CMakeFiles/md.dir/rf_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/rf_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite3FD': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:703: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite_f': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1188: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'count_intercg_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1344: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'get_vsite_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1383: warning: unused variable 'cg_c' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'init_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1494: warning: unused variable 'cg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c: In function 'RF_excl_correction': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c:58: warning: unused variable 'top' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c: In function 'update_QMMMrec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c:740: warning: unused variable 'MMatoms' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c:140: warning: 'int_comp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 61 [ 61%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_parallel_3dfft.c.o Building C object src/mdlib/CMakeFiles/md.dir/domdec_box.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_box.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_box.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c:46: warning: 'copy_int_array' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c:57: warning: 'make_slab2grid' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/pppm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pppm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c: In function 'gmx_pppm_init': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:508: warning: unused variable 'spacing' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:508: warning: unused variable 'box_diag' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:507: warning: unused variable 'tol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:506: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:506: warning: unused variable 'r1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:505: warning: unused variable 'grids' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'porder' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'nz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'nx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 61%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/mdlib/CMakeFiles/md.dir/shellfc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/shellfc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/minimize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/minimize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'predict_shells': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:118: warning: unused variable 'dt_3' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:118: warning: unused variable 'dt_2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'init_shell_flexcon': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:200: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'init_adir': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:689: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:689: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:686: warning: unused variable 'scale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'gt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'ga' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'gf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'relax_shell_flexcon': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:777: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:772: warning: unused variable 'xiS' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:772: warning: unused variable 'xiH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:770: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'get_f_norm_max': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:185: warning: unused variable 'fmax2_0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:909: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:895: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:894: warning: unused variable 'sfm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_lbfgs': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:1431: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_steep': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2059: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2049: warning: unused variable 'dvdlambda' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2048: warning: unused variable 'constepsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_nm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2269: warning: unused variable 'fmax' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2269: warning: unused variable 'fnorm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2255: warning: unused variable 'bNS' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:569: warning: 'do_x_step' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:591: warning: 'do_x_sub' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/shakef.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/shakef.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'cshake': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tiz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tiy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tix' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'vec_shakef': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'rvscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'rscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'vscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'crattle': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tiz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tiy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tix' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'jmdt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'imdt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'diff' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'rijd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:456: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:454: warning: unused variable 'mytol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:83: warning: 'pv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/md_support.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/md_support.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/ebin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ebin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c: In function 'compute_globals': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:297: warning: unused variable 'temp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:297: warning: unused variable 'ekin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:294: warning: unused variable 'bVV' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:293: warning: unused variable 'shakeall_vir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c: In function 'add_ebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:127: warning: unused variable 'sigma' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:127: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:54: warning: 'rms_ener' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 62 [ 62%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/vcm.c.o Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall_sse2_double.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/vcm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'calc_vcm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'zz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'yz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'yy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'do_stopcm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:170: warning: unused variable 'tm_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:170: warning: unused variable 'tm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:169: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'check_cm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:249: warning: unused variable 'Tcm' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/fft5d.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/fft5d.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/fft5d.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/fft5d.c:115: warning: 'lpfactor' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/constr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/constr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'too_many_constraint_warnings': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:185: warning: unused variable 'abort' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'constrain': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:306: warning: unused variable 'vstor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:304: warning: unused variable 'ncons' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:303: warning: unused variable 'd' [ 62%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'init_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:955: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'inter_charge_group_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:1120: warning: unused variable 'nat' Building C object src/mdlib/CMakeFiles/md.dir/perf_est.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/perf_est.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:163: warning: 'icomp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c: In function 'pme_load_estimate': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c:91: warning: unused variable 'fljtab' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/nsgrid.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/nsgrid.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'set_grid_sizes': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:206: warning: unused variable 'stddev' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:206: warning: unused variable 'av' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'init_grid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:361: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:361: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'grid_first': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:474: warning: unused variable 'cx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/wnblist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/wnblist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: In function 'read_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'icmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'full' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'nnbl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:136: warning: unused variable 'b2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:136: warning: unused variable 'b1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:135: warning: unused variable 'bNL' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: In function 'dump_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:234: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 63 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 63%] [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mvxvf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mvxvf.c Building C object src/mdlib/CMakeFiles/md.dir/pme_pp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pme_pp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme_pp.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 63%] [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ewald.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c Building C object src/mdlib/CMakeFiles/md.dir/edsam.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/edsam.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/edsam.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c: In function 'init_ewald_tab': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c:105: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/qm_gamess.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_gamess.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_gamess.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 63%] [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftpack.c.o Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_xml.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_qhop_xml.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftpack.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftpack.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/csettle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/csettle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 64 [ 64%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'qhop_process_attr': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:182: warning: unused variable 'eprop' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'qhop_process_tree': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:247: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'gmx_qhops_read': Building C object src/mdlib/CMakeFiles/md.dir/domdec_network.c.o /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:279: warning: unused variable 'npd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:279: warning: unused variable 'i' cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_network.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_network.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'add_xml_qhop': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:311: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:310: warning: unused variable 'comp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:310: warning: unused variable 'grandchild' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'gmx_qhops_write': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:333: warning: unused variable 'nmt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'settle_proj': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:189: warning: unused variable 'kfacHH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:189: warning: unused variable 'kfacOH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:188: warning: unused variable 'invvscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:187: warning: unused variable 'derpm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'xshake': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:305: warning: unused variable 'conv' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'csettle': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:417: warning: unused variable 'shakeret' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 64%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/mdlib/CMakeFiles/md.dir/wall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/wall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/genborn.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c: In function 'do_walls': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c:109: warning: unused variable 'Heps' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'init_gb_still': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'rbc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'rab' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'cosine' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'factor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p3' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:205: warning: unused variable 'rk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:205: warning: unused variable 'r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:204: warning: unused variable 'angle' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:204: warning: unused variable 'length' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:202: warning: unused variable 'ibm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:202: warning: unused variable 'iam' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'at' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'idx2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'id' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'ic' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nang' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nbond' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'init_gb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:390: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'ai' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_still': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:518: warning: unused variable 'dr4' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:518: warning: unused variable 'dr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:515: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_hct': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:656: warning: unused variable 'duij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:652: warning: unused variable 'gpi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:649: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:649: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_obc': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:875: warning: unused variable 'duij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:872: warning: unused variable 'min_rad' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:872: warning: unused variable 'rad' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:871: warning: unused variable 'gpi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:868: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:868: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1094: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'gb_bonds_tab': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1346: warning: unused variable 'dvdaj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1346: warning: unused variable 'vcoul' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1339: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_nonpolar': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1477: warning: unused variable 'rbi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_chainrule': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1550: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1548: warning: unused variable 'rinv11' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1547: warning: unused variable 'rsq11' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1546: warning: unused variable 'rb2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1546: warning: unused variable 'fij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_forces': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1663: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1661: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'make_gb_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1887: warning: unused variable 'apa' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1875: warning: 'compare_int' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/forcerec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/forcerec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin_bar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdebin_bar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin_bar.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'check_solvent_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:164: warning: unused variable 'excl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'set_avcsixtwelve': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:769: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin_bar.c:99: warning: 'mde_delta_h_free' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'init_forcerec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1299: warning: unused variable 'ngrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1299: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1235: warning: 'forcerec_check_sse2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/init.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/init.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c: In function 'set_state_entries': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c:73: warning: unused variable 'nnhpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c:64: warning: 'int_title' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_con.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_con.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: In function 'dd_make_local_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c:950: warning: unused variable 'gat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: In function 'init_domdec_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c:1074: warning: unused variable 'dc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 65 [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/nlistheuristics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/nlistheuristics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nlistheuristics.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/clincs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/clincs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: In function 'do_lincsp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'lam' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'wfac' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'rlen' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: In function 'constrain_lincs': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:1165: warning: unused variable 'error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:1114: warning: 'dump_conf' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/tgroup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tgroup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/pull.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pull.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: In function 'init_grptcstat': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c:56: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: In function 'sum_ekin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c:204: warning: unused variable 'ek' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: In function 'get_pullgrps_dr': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:301: warning: unused variable 'pref' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: In function 'do_constraint': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:458: warning: unused variable 'mass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:457: warning: unused variable 'd0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/calcvir.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c:46: warning: 'dprod1' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c:159: warning: 'lo_fcv2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_parm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_qhop_parm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_parm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcmu.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/calcmu.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcmu.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/groupcoord.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/groupcoord.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/groupcoord.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 66 [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/stat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/stat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/stat.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: In function 'setup_gb_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:119: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:116: warning: unused variable 'nj1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:116: warning: unused variable 'nj0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:114: warning: unused variable 'tp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: In function 'genborn_allvsall_setup': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:330: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'print_missing_interactions_mb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:114: warning: unused variable 'a_gl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:114: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'global_atomnr_to_moltype_ind': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:364: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'count_excls': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:379: warning: unused variable 'n_inter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_make_reverse_top': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:628: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:628: warning: unused variable 'n_recursive_vsite' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'add_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:772: warning: unused variable 'iatoms_r' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'make_local_exclusions': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1234: warning: unused variable 'a_loc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_make_local_top': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1422: warning: unused variable 'bUniqueExcl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_init_local_state': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1576: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1576: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'check_link': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1616: warning: unused variable 'aj' [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/update.c.o /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/update.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'do_update_vv_vel': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vnrel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'va' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vv' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vn' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'u' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:237: warning: unused variable 'vrel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:236: warning: unused variable 'gt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:235: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'do_update_vv_pos': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:287: warning: unused variable 'w_dt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:287: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_tcouple': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'homenr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1303: warning: unused variable 'vbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1298: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1298: warning: unused variable 'bExtended' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_box': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1470: warning: unused variable 'vir_con' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1469: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1468: warning: unused variable 'dt_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bEner' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bLog' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bLastStep' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_coords': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xprimein' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xpall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'fall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'forcein' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xcom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vcom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1587: warning: unused variable 'vir_con' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1586: warning: unused variable 'icom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nexpand' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nconstr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nsettle' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nshake' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'jatom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'iatom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'blen1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'blen0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1581: warning: unused variable 'imassin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1581: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bEner' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bLog' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bLastStep' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used [ 66%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/domdec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_move_cellx': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:982: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:982: warning: unused variable 'dim1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_collect_vec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1432: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1430: warning: unused variable 'ma' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_distribute_vec_scatterv': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1667: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_distribute_state': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1709: warning: unused variable 'ngtcp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1709: warning: unused variable 'ngtch' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'gmx_ddcoord2pmeindex': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2075: warning: unused variable 'nc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2075: warning: unused variable 'coords_pme' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'make_dd_indices': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2393: warning: unused variable 'ga2la' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'check_bLocalCG': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2449: warning: unused variable 'ncg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'set_dd_cell_sizes_dlb_root': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3183: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'distribute_dd_cell_sizes_dlb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3365: warning: unused variable 'dim1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'distribute_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3657: warning: unused variable 'bUnbounded' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3653: warning: unused variable 'box_size' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3651: warning: unused variable 'npbcdim' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_redistribute_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4177: warning: unused variable 'cell_d' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4177: warning: unused variable 'd4' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'get_load_distribution': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4849: warning: unused variable 'cid' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'setup_dd_grid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:5309: warning: unused variable 'bZYX' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'check_dlb_support': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6039: warning: unused variable 'dd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'init_domain_decomposition': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'd' [ 66%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_init_bondeds': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6694: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6693: warning: unused variable 'bBondComm' Building C object src/mdlib/CMakeFiles/md.dir/domdec_setup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_setup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'setup_dd_communication': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'inv_ncg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r2inc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_scomm2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_mb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_partition_system': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:8178: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:291: warning: 'ga2la_get_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'guess_npme': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:145: warning: unused variable 'ir_try' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:144: warning: unused variable 'nky' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:144: warning: unused variable 'nkx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'comm_cost_est': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:298: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'assign_factors': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:486: warning: unused variable 'z' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/ghat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ghat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ghat.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 67 [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tables.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'done_tabledata': /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:483: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'make_tables': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:868: warning: unused variable 'j' [ 67%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'make_gb_table': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:991: warning: unused variable 'x0_r2_error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:991: warning: unused variable 'x0_r_error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:990: warning: unused variable 'rel_error_r2_old' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:990: warning: unused variable 'rel_error_r_old' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:989: warning: unused variable 'rel_error_r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:989: warning: unused variable 'rel_error_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:988: warning: unused variable 'abs_error_r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:988: warning: unused variable 'abs_error_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'tabsel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:977: warning: unused variable 'fns14' [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/pullutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pullutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:159: warning: 'splint' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/ns.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ns.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: In function 'pull_set_pbcatom': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c:85: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: In function 'pull_calc_coms': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c:281: warning: unused variable 'xx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'init_neighbor_list': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:248: warning: unused variable 'solvent' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'new_i_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'nshift' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'put_in_list_at': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:640: warning: unused variable 'rlj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:640: warning: unused variable 'qq' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:635: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:633: warning: unused variable 'ind_ij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_inner_tric': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1466: warning: unused variable 'nsbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_inner_rect': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1499: warning: unused variable 'nsbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_simple_core': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'i0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'jcg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'nsgrid_core': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1949: warning: unused variable 'xi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1945: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'init_ns': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2402: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'search_neighbours': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2528: warning: unused variable 'cg_end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2528: warning: unused variable 'cg_start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2527: warning: unused variable 'i_egp_flags' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2526: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2522: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2522: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1637: warning: 'get_dx' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/qm_gaussian.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_gaussian.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_gaussian.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/tpi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tpi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c: In function 'do_tpi': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:160: warning: unused variable 'dvdl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:150: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:150: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:135: warning: unused variable 'TPI' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_mopac.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_mopac.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 68 [ 68%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_wallcycle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_wallcycle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_wallcycle.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 68%] Building C object src/mdlib/CMakeFiles/md.dir/pme.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pme.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'pmeredist_pd': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:399: warning: unused variable 'idxa' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'copy_pmegrid_to_fftgrid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:851: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'copy_fftgrid_to_pmegrid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:917: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'spread_q_bsplines': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1105: warning: unused variable 'bndsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1105: warning: unused variable 'localsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1100: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1099: warning: unused variable 'ol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'init_atomcomm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 'nk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'init_overlap_comm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1854: warning: unused variable 'nk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1854: warning: unused variable 'nn' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1853: warning: unused variable 'exten' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'maxlr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'rbnd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'lbnd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'gmx_pme_init': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2039: warning: unused variable 'atc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'gmx_pme_do': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2468: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2464: warning: unused variable 'local_ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'nz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'nx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2004: warning: 'gmx_pme_check_grid_restrictions' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 68%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_single.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_sse2_single.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_sse2_single.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 68%] Building C object src/mdlib/CMakeFiles/md.dir/force.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/force.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: In function 'ns': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:86: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: In function 'do_force_lowlevel': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:147: warning: unused variable 'dvdgb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:141: warning: unused variable 'bDoEpot' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Linking C shared library libmd.so cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /usr/bin/gcc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/iteratedconstraints.c.o CMakeFiles/md.dir/gmx_fft_fftw2.c.o CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/domdec_box.c.o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/pppm.c.o CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/minimize.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/constr.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/nsgrid.c.o CMakeFiles/md.dir/wnblist.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/ewald.c.o CMakeFiles/md.dir/edsam.c.o CMakeFiles/md.dir/qm_gamess.c.o CMakeFiles/md.dir/gmx_qhop_xml.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/wall.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/forcerec.c.o CMakeFiles/md.dir/mdebin_bar.c.o CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/calcvir.c.o CMakeFiles/md.dir/gmx_qhop_parm.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/update.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/ghat.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/pullutil.c.o CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/force.c.o ../gmxlib/libgmx.so.6 -ldl -lm -lfftw3f -lxml2 -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib && /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 59 60 61 62 63 64 65 66 67 68 [ 68%] Built target md make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/depend make -f src/tools/CMakeFiles/gmxana.dir/build.make src/tools/CMakeFiles/gmxana.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/gmxana.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxpreprocess.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/gmxana.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/gmxana.dir/depend.internal". Scanning dependencies of target gmxpreprocess make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 68%] [ 68%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 68%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/compute_io.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/compute_io.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/add_par.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/add_par.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/add_par.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/convparm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/convparm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c: In function 'compute_io': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c:61: warning: unused variable 'nfep' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'assign_param': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:96: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'new_interaction_list': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:459: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'convert_params': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:469: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:457: warning: 'new_interaction_list' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 68%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gen_ad.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gen_ad.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'get_impropers': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:437: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:436: warning: unused variable 'hbidih' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:434: warning: unused variable 'a0' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'clean_excls': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:576: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:576: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'generate_excls': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'e' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'l1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'k1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'j1' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:114: warning: 'aeq' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:289: warning: 'ideq' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:327: warning: 'dump_param' defined but not used Scanning dependencies of target gmxana make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/gmxana.dir/build.make src/tools/CMakeFiles/gmxana.dir/build [ 68%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'read_vsite_database': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:150: warning: unused variable 'prevdir' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:150: warning: unused variable 'j' [ 68%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/genhydro.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/genhydro.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'add_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:487: warning: unused variable 'bb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'gen_vsites_trp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:759: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:758: warning: unused variable 'mtot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:758: warning: unused variable 'mwtot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:756: warning: unused variable 'xM' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:747: warning: unused variable 'dist' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:746: warning: unused variable 'I' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'gen_vsites_tyr': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:986: warning: unused variable 'vmass' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'do_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:1350: warning: unused variable 'bb' make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 68%] Building C object src/tools/CMakeFiles/gmxana.dir/autocorr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/autocorr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/autocorr.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'expand_hackblocks_one': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:161: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'check_atoms_present': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:275: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'add_h_low': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:390: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 70 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 69%] [ 69%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gpp_bond_atomtype.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gpp_atomtype.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 69%] Building C object src/tools/CMakeFiles/gmxana.dir/expfit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/expfit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/expfit.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 69%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/h_db.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/h_db.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/expfit.c:90: warning: 'signum' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: In function 'dump_h_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:117: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: In function 'read_h_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:200: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:113: warning: 'dump_h_db' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 69%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/hackblock.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/hackblock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hackblock.c [ 69%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/hizzie.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/hizzie.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c: In function 'set_histp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:195: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:192: warning: unused variable 'his0' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:192: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:188: warning: unused variable 'bHaveH' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 86 [ 70%] Building C object src/tools/CMakeFiles/gmxana.dir/polynomials.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/polynomials.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/polynomials.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 70%] Building C object src/tools/CMakeFiles/gmxana.dir/levenmar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/levenmar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:78: warning: 'dvector' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:106: warning: 'dmatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:123: warning: 'imatrix1' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:141: warning: 'submatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:168: warning: 'free_dvector' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:183: warning: 'free_dmatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:191: warning: 'free_imatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:201: warning: 'free_submatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:208: warning: 'convert_matrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:224: warning: 'free_convert_matrix' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 70%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/gmxana.dir/anadih.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/anadih.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/anadih.c [ 70%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/nm2type.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/nm2type.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: In function 'rd_nm2type_file': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c:72: warning: unused variable 'blen' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: In function 'nm2type': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c:179: warning: unused variable 'quality' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 70%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/pdb2top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/pdb2top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 71 [ 70%] [ 71%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/pgutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/pgutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pgutil.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/readir.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/readir.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'missing_atoms': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:85: warning: unused variable 'bRet' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'print_top_comment': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:539: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'get_hackblocks_rtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:983: warning: unused variable 'bC' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:983: warning: unused variable 'bN' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:981: warning: unused variable 'Hnum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:980: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'match_atomnames_with_rtp_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1160: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'match_atomnames_with_rtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1324: warning: unused variable 'bFoundInAdd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1323: warning: unused variable 'start_nr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1322: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1322: warning: unused variable 'start_at' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1321: warning: unused variable 'anmnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1320: warning: unused variable 'hbr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1317: warning: unused variable 'newnm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1316: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'gen_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1354: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1354: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:743: warning: 'inter_res_bond' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'check_ir': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:162: warning: unused variable 'ns_type' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'do_index': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:1782: warning: unused variable 'SAtime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'triple_check': [ 71%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:2293: warning: unused variable 'npct' Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/readpull.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/readpull.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c: In function 'read_pullparams': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c:107: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c:103: warning: unused variable 'nchar' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 71%] Building C object src/tools/CMakeFiles/gmxana.dir/pp2shift.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/pp2shift.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/pp2shift.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 71%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/resall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/resall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c: In function 'read_resall': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c:256: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c:482: warning: 'neq_str' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 71%] Building C object src/tools/CMakeFiles/gmxana.dir/dlist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/dlist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/dlist.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/dlist.c: In function 'mk_dlist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/dlist.c:52: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/dlist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 71%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/sorting.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/sorting.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/sorting.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 71%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/specbond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/specbond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/specbond.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 71%] Building C object src/tools/CMakeFiles/gmxana.dir/eigio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/eigio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigio.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 71%] [ 71%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/ter_db.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/ter_db.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c Building C object src/tools/CMakeFiles/gmxana.dir/cmat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/cmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/cmat.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'read_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:84: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'print_ter_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:136: warning: unused variable 'nname' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'filter_ter': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:375: warning: unused variable 's2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:373: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 71%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/tomorse.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/tomorse.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tomorse.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 71%] Building C object src/tools/CMakeFiles/gmxana.dir/eigensolver.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/eigensolver.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c: In function 'eigensolver': /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c:64: warning: unused variable 'iu' /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c:64: warning: unused variable 'il' /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 87 [ 72%] Building C object src/tools/CMakeFiles/gmxana.dir/nsc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/nsc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 72%] Building C object src/tools/CMakeFiles/gmxana.dir/hxprops.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/hxprops.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/hxprops.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 72 [ 73%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topdirs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topdirs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topdirs.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c: In function 'nsc_dclm_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c:660: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c:540: warning: unused variable 'jat_xx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/hxprops.c: In function 'ellipticity': /builddir/build/BUILD/gromacs-4.5.5/src/tools/hxprops.c:84: warning: unused variable 'Xi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/hxprops.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topexcl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topexcl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c: In function 'generate_excl': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/fitahx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/fitahx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/fitahx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: In function 'generate_gb_exclusion_interactions': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n14' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n13' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:389: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:389: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: In function 'read_topol': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:517: warning: unused variable 'block' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/geminate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/geminate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: In function 'init_gemParams': /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:672: warning: statement with no effect /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: In function 'fitGemRecomb': /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:751: warning: unused variable 'dumpname' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:751: warning: unused variable 'dumpstr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:750: warning: unused variable 'GD' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:749: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:749: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:748: warning: unused variable 'dumpdata' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:748: warning: unused variable 'tol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:748: warning: unused variable 'd2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:748: warning: unused variable 'size' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'maxiter' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'iter' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'nThreads' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: In function 'takeAwayBallistic': /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1019: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1018: warning: unused variable 'sorted' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1017: warning: unused variable 'ddt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1016: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1015: warning: unused variable 'A' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1014: warning: unused variable 'guess' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1013: warning: unused variable 'BD' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1012: warning: unused variable 'iter' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1012: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1012: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: In function 'fixGemACF': /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1257: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.h:5: warning: 'gemType' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:96: warning: 'gem_Re' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:97: warning: 'gem_Im' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:191: warning: 'gem_cxintpow' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:268: warning: 'gem_cxrsqrt' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:288: warning: 'gem_cxprintf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:424: warning: 'gem_W' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:434: warning: 'gem_cerf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:540: warning: 'gem_cW' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:557: warning: 'eq10v2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:611: warning: 'getLogIndex' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1221: warning: 'd2r' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_analyze.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_analyze.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c: In function 'luzar_correl': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:631: warning: unused variable 'weight' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:629: warning: unused variable 'tol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c: In function 'gmx_analyze': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:1064: warning: unused variable 'gemfile' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:984: warning: unused variable 'rcut' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:984: warning: unused variable 'diffusion' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:983: warning: unused variable 'nFitPoints' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:982: warning: unused variable 'bLuzarError' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.h:5: warning: 'gemType' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:323: warning: 'anal_ee' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:836: warning: 'do_geminate' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] [ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_anaeig.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_anaeig.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/toppush.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/toppush.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_nbt': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:794: warning: unused variable 'sig6' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:792: warning: unused variable 'atnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:787: warning: unused variable 'form2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_cmaptype': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:920: warning: unused variable 'bAllowRepeat' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:915: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'default_cmap_params': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1312: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_bond': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: In function 'calc_entropy_schlitter': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:98: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:97: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:97: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:97: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:96: warning: unused variable 'indx' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1485: warning: unused variable 'paramB' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: In function 'compare': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:229: warning: unused variable 'nrow' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'param_defB' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'param_defA' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'paramB' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: In function 'rmsf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:717: warning: unused variable 'nrow' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: In function 'gmx_anaeig': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:860: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:859: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:859: warning: unused variable 'xid' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:857: warning: unused variable 'xread' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:857: warning: unused variable 'x' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:850: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:850: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:849: warning: unused variable 'out' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_angle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_angle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c: In function 'gmx_g_angle': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:150: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:146: warning: unused variable 'fraction' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:146: warning: unused variable 'aa' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:146: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:141: warning: unused variable 'angind' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:141: warning: unused variable 'nat2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:141: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:141: warning: unused variable 'total' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:138: warning: unused variable 'Jc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:135: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:134: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topshake.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topshake.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 88 [ 74%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_bond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bond.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c: In function 'make_shake': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c:98: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c:98: warning: unused variable 'nb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 74%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/toputil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/toputil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toputil.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toputil.c:175: warning: 'print_nbt' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 74%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_bundle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c: In function 'dump_axes': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c:143: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c: In function 'gmx_bundle': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c:215: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c:211: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c:200: warning: unused variable 'out' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 74%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 74%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_chi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_chi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_block': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_blocka': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:321: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:320: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_top': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_groups': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:376: warning: unused variable 'ndiff' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'comp_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:715: warning: unused variable 'sh' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'comp_enx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:1048: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:1045: warning: unused variable 'block' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c: In function 'histogramming': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c:424: warning: unused variable 'his_aa1' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 74%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c: In function 'gmx_chi': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c:1136: warning: unused variable 'j' Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 74%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_cluster.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_cluster.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_cluster.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'vsitetype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_angles': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'vsitetype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_dihs': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'ftype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_cluster.c: In function 'mark_clusters': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_cluster.c:644: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_cluster.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 74%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_confrms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_confrms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c: In function 'find_matching_names': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:259: warning: unused variable 'atnm2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:259: warning: unused variable 'atnm1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:259: warning: unused variable 'resnm2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:259: warning: unused variable 'resnm1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:256: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:254: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c: In function 'gmx_confrms': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:419: warning: unused variable 'tmas2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:419: warning: unused variable 'tmas1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:416: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 74%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_covar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_covar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 73 [ 75%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/fflibutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/fflibutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c: In function 'gmx_covar': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c:144: warning: unused variable 'count' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c:143: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c:143: warning: unused variable 'ntopatoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c:133: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c: At top level: /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used [ 75%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/xlate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/xlate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xlate.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c: In function 'low_fflib_search_file_end': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:159: warning: unused variable 'pdum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:153: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:151: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 75%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_current.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_current.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c Linking C shared library libgmxpreprocess.so cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess.dir/link.txt --verbose=1 /usr/bin/gcc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libgmxpreprocess.so.6 -o libgmxpreprocess.so.6 CMakeFiles/gmxpreprocess.dir/add_par.c.o CMakeFiles/gmxpreprocess.dir/compute_io.c.o CMakeFiles/gmxpreprocess.dir/convparm.c.o CMakeFiles/gmxpreprocess.dir/gen_ad.c.o CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o CMakeFiles/gmxpreprocess.dir/genhydro.c.o CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o CMakeFiles/gmxpreprocess.dir/h_db.c.o CMakeFiles/gmxpreprocess.dir/hackblock.c.o CMakeFiles/gmxpreprocess.dir/hizzie.c.o CMakeFiles/gmxpreprocess.dir/nm2type.c.o CMakeFiles/gmxpreprocess.dir/pdb2top.c.o CMakeFiles/gmxpreprocess.dir/pgutil.c.o CMakeFiles/gmxpreprocess.dir/readir.c.o CMakeFiles/gmxpreprocess.dir/readpull.c.o CMakeFiles/gmxpreprocess.dir/resall.c.o CMakeFiles/gmxpreprocess.dir/sorting.c.o CMakeFiles/gmxpreprocess.dir/specbond.c.o CMakeFiles/gmxpreprocess.dir/ter_db.c.o CMakeFiles/gmxpreprocess.dir/tomorse.c.o CMakeFiles/gmxpreprocess.dir/topdirs.c.o CMakeFiles/gmxpreprocess.dir/topexcl.c.o CMakeFiles/gmxpreprocess.dir/topio.c.o CMakeFiles/gmxpreprocess.dir/toppush.c.o CMakeFiles/gmxpreprocess.dir/topshake.c.o CMakeFiles/gmxpreprocess.dir/toputil.c.o CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o CMakeFiles/gmxpreprocess.dir/fflibutil.c.o CMakeFiles/gmxpreprocess.dir/xlate.c.o ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -lpthread -ldl -lm -lfftw3f -lxml2 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 75%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c: In function 'calc_mjdsp': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:271: warning: unused variable 'rfr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:270: warning: unused variable 'rtmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c: In function 'dielectric': Building C object src/tools/CMakeFiles/gmxana.dir/gmx_density.c.o /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:333: warning: unused variable 'qtmp' cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_density.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:315: warning: unused variable 'dm_d' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:315: warning: unused variable 'dm_s' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:305: warning: unused variable 'rfr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:300: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:299: warning: unused variable 'f' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:299: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:299: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c: In function 'gmx_current': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:732: warning: unused variable 'tfile' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:731: warning: unused variable 'outi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:728: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:727: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:726: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:725: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:725: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:725: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:723: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_symlink_library libgmxpreprocess.so.6 libgmxpreprocess.so.6 libgmxpreprocess.so make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 70 71 72 73 [ 75%] Built target gmxpreprocess make -f src/kernel/CMakeFiles/g_luck.dir/build.make src/kernel/CMakeFiles/g_luck.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_luck.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_luck.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_luck.dir/depend.internal". Scanning dependencies of target g_luck make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/g_luck.dir/build.make src/kernel/CMakeFiles/g_luck.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 75%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c: In function 'calc_density': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:259: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:254: warning: unused variable 'ax2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:254: warning: unused variable 'ax1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:252: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:251: warning: unused variable 'slCount' Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_luck.dir/g_luck.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_luck.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used Linking C executable g_luck cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_luck.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_luck.dir/g_luck.c.o -o g_luck -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 89 [ 76%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_densmap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_densmap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densmap.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 76%] Built target g_luck make -f src/kernel/CMakeFiles/g_protonate.dir/build.make src/kernel/CMakeFiles/g_protonate.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_protonate.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_protonate.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_protonate.dir/depend.internal". Scanning dependencies of target g_protonate make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/g_protonate.dir/build.make src/kernel/CMakeFiles/g_protonate.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used [ 76%] /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Building C object src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_protonate.dir/g_protonate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_protonate.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 76%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dih.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dih.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dih.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dih.c:56: warning: 'dump_dih' defined but not used Linking C executable g_protonate cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_protonate.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_protonate.dir/g_protonate.c.o -o g_protonate -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 76%] Built target g_protonate make -f src/kernel/CMakeFiles/g_x2top.dir/build.make src/kernel/CMakeFiles/g_x2top.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_x2top.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_x2top.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_x2top.dir/depend.internal". Scanning dependencies of target g_x2top make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/g_x2top.dir/build.make src/kernel/CMakeFiles/g_x2top.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 76%] Building C object src/kernel/CMakeFiles/g_x2top.dir/g_x2top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_x2top.dir/g_x2top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 76%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dielectric.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dielectric.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 76%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_kinetics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_kinetics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_kinetics.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c: In function 'set_cgnr': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:177: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c: In function 'set_force_const': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:254: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:425: warning: unused variable 'scale' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:415: warning: unused variable 'cutoff' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'ndih' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:410: warning: unused variable 'nres' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:79: warning: 'set_x_blen' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:116: warning: 'get_atype' defined but not used [ 76%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c: In function 'calc_nbegin': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c:62: warning: unused variable 'dtt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c:62: warning: unused variable 'dt' Building C object src/tools/CMakeFiles/gmxana.dir/gmx_spatial.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_spatial.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 76%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_tune_pme.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_tune_pme.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tune_pme.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c: In function 'gmx_spatial': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c:134: warning: unused variable 'shx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c:106: warning: unused variable 'bSHIFT' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 76%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dipoles.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dipoles.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'do_gkr': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:159: warning: unused variable 'r2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:158: warning: unused variable 'index' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'print_gkrbin': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:296: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:296: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'mol_quad': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:425: warning: unused variable 'rcom_n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:425: warning: unused variable 'rcom_m' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'compute_avercos': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:589: warning: unused variable 'n5' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:589: warning: unused variable 'dc1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'do_dip': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:916: warning: unused variable 'gi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:1196: warning: unused variable 'mm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:1187: warning: unused variable 'lsq' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'Vol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'Msq' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'Mz' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'My' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'Mx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:683: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:682: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:680: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:678: warning: unused variable 'nmol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:678: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:678: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'gmx_dipoles': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:1352: warning: unused variable 'bCorr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:1307: warning: unused variable 'bMolCorr' Linking C executable g_x2top /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_x2top.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_x2top.dir/g_x2top.c.o -o g_x2top -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 90 [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_disre.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_disre.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_disre.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 77%] Built target g_x2top make -f src/kernel/CMakeFiles/gmxcheck.dir/build.make src/kernel/CMakeFiles/gmxcheck.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxcheck.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxcheck.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxcheck.dir/depend.internal". Scanning dependencies of target gmxcheck make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/gmxcheck.dir/build.make src/kernel/CMakeFiles/gmxcheck.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 77%] Building C object src/kernel/CMakeFiles/gmxcheck.dir/gmxcheck.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxcheck.dir/gmxcheck.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_disre.c: In function 'dump_disre_matrix': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_disre.c:450: warning: unused variable 'iii' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_disre.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'tpx2system': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:89: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'tpx2methods': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:135: warning: unused variable 'sh' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'chk_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:198: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'chk_trj': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:249: warning: unused variable 'bOK' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:248: warning: unused variable 'prec' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:248: warning: unused variable 'tt' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:248: warning: unused variable 'rdum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'chk_ndx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:523: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'chk_enx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:547: warning: unused variable 'ndr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Linking C executable gmxcheck cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxcheck.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/gmxcheck.dir/gmxcheck.c.o -o gmxcheck -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 77%] Built target gmxcheck make -f src/kernel/CMakeFiles/gmxdump.dir/build.make src/kernel/CMakeFiles/gmxdump.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxdump.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxdump.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxdump.dir/depend.internal". Scanning dependencies of target gmxdump make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/gmxdump.dir/build.make src/kernel/CMakeFiles/gmxdump.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 69 [ 78%] Building C object src/kernel/CMakeFiles/gmxdump.dir/gmxdump.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxdump.dir/gmxdump.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c: In function 'gmx_dist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c:102: warning: unused variable 'fplt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c:94: warning: unused variable 'aid' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c:88: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c: In function 'list_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:150: warning: left-hand operand of comma expression has no effect /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:99: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c: In function 'list_ene': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:326: warning: unused variable 'rav' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:320: warning: unused variable 'ndr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:64: warning: 'dump_top' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 78%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dyndom.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dyndom.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c: In function 'rot_conf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:61: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:59: warning: unused variable 'temp43' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:59: warning: unused variable 'temp21' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:59: warning: unused variable 'temp4' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:58: warning: unused variable 'Tx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:58: warning: unused variable 'Tinvcm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:58: warning: unused variable 'Tcm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:56: warning: unused variable 'center' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 78%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_enemat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_enemat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_enemat.c Linking C executable gmxdump cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxdump.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/gmxdump.dir/gmxdump.c.o -o gmxdump -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 69 [ 78%] Built target gmxdump make -f src/kernel/CMakeFiles/grompp.dir/build.make src/kernel/CMakeFiles/grompp.dir/depend /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/grompp.dir/DependInfo.cmake --color= /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used [ 78%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/grompp.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/grompp.dir/depend.internal". Building C object src/tools/CMakeFiles/gmxana.dir/gmx_energy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_energy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Scanning dependencies of target grompp make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/grompp.dir/build.make src/kernel/CMakeFiles/grompp.dir/build /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 78%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/gmxana.dir/gmx_lie.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_lie.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_lie.c [ 78%] Building C object src/kernel/CMakeFiles/grompp.dir/grompp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/grompp.dir/grompp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'select_by_name': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:160: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'calc_averages': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:600: warning: unused variable 'steps' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'remove_drift': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:848: warning: unused variable 'sd2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:848: warning: unused variable 'sd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:848: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'calc_fluctuation_props': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:880: warning: unused variable 'vv2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:880: warning: unused variable 'hh2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'analyse_ener': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1032: warning: unused variable 'chi2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1031: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1030: warning: unused variable 'x1mk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1030: warning: unused variable 'x1m' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'fstep' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'diffav' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'diffsum' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'oldfrac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'sfrac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1025: warning: unused variable 'xxx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'fec': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1279: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1279: warning: unused variable 'nre' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'gmx_energy': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1802: warning: unused variable 'nms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1795: warning: unused variable 'ener' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1794: warning: unused variable 'bEDR' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1780: warning: unused variable 'ee' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1774: warning: unused variable 'drout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:139: warning: 'strcount' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: In function 'read_posres': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:712: warning: unused variable 'bFirst' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: In function 'gen_posres': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:839: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:839: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: In function 'init_cmap_grid': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1012: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1249: warning: unused variable 'born' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1248: warning: unused variable 'gb_plist' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1247: warning: unused variable 'n14' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1247: warning: unused variable 'n13' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1247: warning: unused variable 'n12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1236: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 78%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_filter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_filter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_filter.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/mdrun.dir/depend.internal". Scanning dependencies of target mdrun make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 78%] Building C object src/kernel/CMakeFiles/mdrun.dir/gctio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/gctio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gctio.c make -f src/kernel/CMakeFiles/pdb2gmx.dir/build.make src/kernel/CMakeFiles/pdb2gmx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/pdb2gmx.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/pdb2gmx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/pdb2gmx.dir/depend.internal". Scanning dependencies of target pdb2gmx make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/pdb2gmx.dir/build.make src/kernel/CMakeFiles/pdb2gmx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 75 [ 79%] Building C object src/kernel/CMakeFiles/pdb2gmx.dir/pdb2gmx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/pdb2gmx.dir/pdb2gmx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c: In function 'rename_resrtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:296: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c: In function 'sort_pdbatoms': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:615: warning: unused variable 'hbr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:1164: warning: unused variable 'bCheckMerge' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:1154: warning: unused variable 'rtp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:180: warning: 'get_cystp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 79%] Building C object src/kernel/CMakeFiles/mdrun.dir/ionize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/ionize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ionize.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Linking C executable grompp cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/grompp.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/grompp.dir/grompp.c.o -o grompp -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 79%] Built target grompp /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 79%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_gyrate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_gyrate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_gyrate.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 79%] Building C object src/kernel/CMakeFiles/mdrun.dir/runner.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/runner.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_gyrate.c: In function 'gmx_gyrate': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_gyrate.c:191: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_gyrate.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c: In function 'mdrunner': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:362: warning: unused variable 'list' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:359: warning: unused variable 'gro' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:348: warning: unused variable 'tmpr2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:348: warning: unused variable 'tmpr1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:342: warning: unused variable 'realtime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:342: warning: unused variable 'nodetime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used make -f src/kernel/CMakeFiles/tpbconv.dir/build.make src/kernel/CMakeFiles/tpbconv.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/tpbconv.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/tpbconv.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/tpbconv.dir/depend.internal". Scanning dependencies of target tpbconv make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/tpbconv.dir/build.make src/kernel/CMakeFiles/tpbconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 79%] Building C object src/kernel/CMakeFiles/tpbconv.dir/tpbconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/tpbconv.dir/tpbconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 74 [ 80%] Building C object src/kernel/CMakeFiles/mdrun.dir/do_gct.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/do_gct.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c:374: warning: unused variable 'nerror' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c:333: warning: unused variable 'gopts' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c:332: warning: unused variable 'irnew' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: In function 'init_coupling': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:62: warning: unused variable 'atj' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:62: warning: unused variable 'ati' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'index' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'nc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: In function 'do_coupling': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:493: warning: unused variable 'bTest' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:491: warning: unused variable 'xi12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:491: warning: unused variable 'xi6' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffa' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:489: warning: unused variable 'rmsf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:461: warning: 'dump_fm' defined but not used Linking C executable pdb2gmx cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/pdb2gmx.dir/pdb2gmx.c.o -o pdb2gmx -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 75 [ 80%] Built target pdb2gmx /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 91 [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_h2order.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_h2order.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_h2order.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_hbond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_hbond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'findMirror': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:584: warning: unused variable 'u' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'add_frames': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:601: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:601: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:601: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:601: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'search_donors': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1040: warning: unused variable 'stop' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1036: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1036: warning: unused variable 'nra' Linking C executable tpbconv cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/tpbconv.dir/link.txt --verbose=1 /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'is_hbond': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1471: warning: unused variable 'ihb' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'do_merge': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1593: warning: unused variable 'pShift' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'merge_hb': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1674: warning: unused variable 'ogrp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1674: warning: unused variable 'grp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1674: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'do_nhb_dist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1736: warning: unused variable 'nhb' /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/tpbconv.dir/tpbconv.c.o -o tpbconv -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'smooth_tail': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2102: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'analyse_corr': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2125: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2125: warning: unused variable 'dgp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2125: warning: unused variable 'dg' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'do_hbac': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2297: warning: unused variable 'fittolerance' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2295: warning: unused variable 'E' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2293: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2291: warning: unused variable 'ptimes' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2283: warning: unused variable 'ght_fac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2283: warning: unused variable 'ct_fac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2283: warning: unused variable 'p_ct' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2281: warning: unused variable 'nhbi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2271: warning: unused variable 'legNN' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2270: warning: unused variable 'iter' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2270: warning: unused variable 'nd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2270: warning: unused variable 'o' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2270: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'gmx_hbond': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:4007: warning: unused variable 'rtmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:4006: warning: unused variable 'itmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3259: warning: unused variable 'threadNr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3258: warning: unused variable 'actual_nThreads' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3258: warning: unused variable 'jj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3257: warning: unused variable 'E' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3251: warning: unused variable 'kcell' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3249: warning: unused variable 'fpins' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3246: warning: unused variable 'bin' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3244: warning: unused variable 'was' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'zkk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'ykk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'xkk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'ak' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'zk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'yk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'xk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'ja' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'id' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3153: warning: unused variable 'NNtype' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3152: warning: unused variable 'logAfterTime' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:899: warning: 'in_list' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1159: warning: 'control_pHist' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1431: warning: 'pbc_correct' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2229: warning: 'parallel_print' defined but not used make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Built target tpbconv /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/repl_ex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/repl_ex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: In function 'init_replica_exchange': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:118: warning: unused variable 'temp' [ 81%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: In function 'replica_exchange': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:725: warning: unused variable 'shift' Building C object src/tools/CMakeFiles/gmxana.dir/gmx_helix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_helix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helix.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:706: warning: 'write_debug_x' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helix.c: In function 'gmx_helix': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helix.c:215: warning: unused variable 'nre' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helix.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_mindist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_mindist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c: In function 'periodic_mindist_plot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:116: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c: In function 'dist_plot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:273: warning: unused variable 'frout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c: In function 'gmx_mindist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:543: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:542: warning: unused variable 'atm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:537: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:502: warning: unused variable 'bugs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/xutils.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/xutils.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/md.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/md.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c: In function 'update_forcefield': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c:334: warning: unused variable 'bDone' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c: In function 'do_md': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:184: warning: unused variable 'iter_i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:179: warning: unused variable 'oldfom' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:179: warning: unused variable 'fom' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:178: warning: unused variable 'tmpvir' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:174: warning: unused variable 'grpname' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:164: warning: unused variable 'timestep' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:140: warning: unused variable 'ebox' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:140: warning: unused variable 'scale_tot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/mdrun.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/mdrun.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_msd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_msd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_msd.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:551: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:503: warning: unused variable 'fptest' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:498: warning: unused variable 'ed' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:387: warning: unused variable 'bPPPME' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:386: warning: unused variable 'bCart' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_msd.c:163: warning: 'done_corr' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/genalg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/genalg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c: In function 'update_ga': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c:196: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/md_openmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c: In function 'do_md_openmm': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c:151: warning: unused variable 'reset_counters_now' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c:151: warning: unused variable 'reset_counters' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_morph.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_morph.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_morph.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_nmeig.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_nmeig.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 92 [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_nmens.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_nmens.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c: In function 'nma_full_hessian': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:144: warning: unused variable 'rdum' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c: In function 'gmx_nmeig': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:318: warning: unused variable 'index' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:316: warning: unused variable 'gnx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:316: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:316: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:315: warning: unused variable 'grpname' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:314: warning: unused variable 'count' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:313: warning: unused variable 'mass_fac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:313: warning: unused variable 'rdum' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:308: warning: unused variable 'ePBC' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:305: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:305: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c: In function 'gmx_nmens': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:107: warning: unused variable 'eigvalnr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:106: warning: unused variable 'invfr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:100: warning: unused variable 'neigval' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:99: warning: unused variable 'totmass' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:90: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:90: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Linking C executable mdrun cd /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/mdrun.dir/gctio.c.o CMakeFiles/mdrun.dir/ionize.c.o CMakeFiles/mdrun.dir/runner.c.o CMakeFiles/mdrun.dir/do_gct.c.o CMakeFiles/mdrun.dir/repl_ex.c.o CMakeFiles/mdrun.dir/xutils.c.o CMakeFiles/mdrun.dir/md.c.o CMakeFiles/mdrun.dir/mdrun.c.o CMakeFiles/mdrun.dir/genalg.c.o CMakeFiles/mdrun.dir/md_openmm.c.o -o mdrun -rdynamic -ldl -lm libgmxpreprocess.so.6 ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread -lfftw3f -lxml2 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 74 [ 82%] [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_order.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_order.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c Built target mdrun /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_principal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_principal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c: In function 'find_nearest_neighbours': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:91: warning: unused variable 'nnb' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:90: warning: unused variable 'mm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:90: warning: unused variable 'm1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:89: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:88: warning: unused variable 'dmat' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:85: warning: unused variable 'dx2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:85: warning: unused variable 'dx1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:84: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:84: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:82: warning: unused variable 'fnsgdist' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:81: warning: unused variable 'fpoutdist' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c: In function 'calc_tetra_order_parm': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:240: warning: unused variable 'subtitle' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:240: warning: unused variable 'fn' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c: In function 'calc_order': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:371: warning: unused variable 'dbangle' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:367: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c: In function 'gmx_principal': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:98: warning: unused variable 'a3' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:98: warning: unused variable 'a2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:98: warning: unused variable 'a1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'mol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'nam' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_polystat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_polystat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_polystat.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_potential.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_potential.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_polystat.c: In function 'calc_int_dist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_polystat.c:82: warning: unused variable 'jj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_polystat.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c: In function 'calc_potential': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c:115: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c:114: warning: unused variable 'slCount' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rama.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rama.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rama.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rdf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rdf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 93 /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c: In function 'do_rdf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'mol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'cur' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:190: warning: unused variable 'mols' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:174: warning: unused variable 'index_cm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:173: warning: unused variable 'isize_cm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:170: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:170: warning: unused variable 'j1' [ 83%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:170: warning: unused variable 'j0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:168: warning: unused variable 'outf2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:168: warning: unused variable 'outf1' Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rms.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rmsf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rmsf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c: In function 'gmx_rmsf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:217: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:216: warning: unused variable 'res0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:211: warning: unused variable 'bCont' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:207: warning: unused variable 'ir' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:206: warning: unused variable 'header' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:204: warning: unused variable 'w_rms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:204: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:203: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:203: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:203: warning: unused variable 'nre' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:203: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:193: warning: unused variable 'bdevX' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rotacf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rotacf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rotacf.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 83%] [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_saltbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_saltbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c Building C object src/tools/CMakeFiles/gmxana.dir/gmx_sas.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_sas.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sas.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c: In function 'gmx_saltbr': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:170: warning: unused variable 'label' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:169: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:169: warning: unused variable 't0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:163: warning: unused variable 'n3' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:163: warning: unused variable 'n2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:163: warning: unused variable 'n1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sas.c: In function 'sas_plot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sas.c:382: warning: unused variable 'mm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sas.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_select.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_select.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_select.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rmsdist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rmsdist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_select.c: In function 'gmx_select': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_select.c:255: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_select.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c: In function 'analyze_noe_equivalent': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c:250: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c: In function 'gmx_rmsdist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c:535: warning: unused variable 'gj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c:535: warning: unused variable 'gi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c:535: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rotmat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rotmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rotmat.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 94 [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_sgangle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_sgangle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sgangle.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 84%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/gmxana.dir/gmx_sorient.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_sorient.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_spol.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_spol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c: In function 'gmx_sorient': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c:115: warning: unused variable 'mtot' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c:115: warning: unused variable 'mass' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c:109: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c: In function 'gmx_spol': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c:169: warning: unused variable 'bPBC' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c:132: warning: unused variable 'xtop' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c:128: warning: unused variable 'title' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_tcaf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_tcaf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c: In function 'gmx_tcaf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c:278: warning: unused variable 'c1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c:268: warning: unused variable 'bTPS' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_traj.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_traj.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_velacc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_velacc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_velacc.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c: In function 'write_pdb_bfac': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c:429: warning: unused variable 'bOne' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c: In function 'gmx_traj': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c:672: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_helixorient.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_helixorient.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c: In function 'gmx_helixorient': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:126: warning: unused variable 'rotangle' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:108: warning: unused variable 'axes' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:107: warning: unused variable 'axes_t0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:94: warning: unused variable 'vproj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:94: warning: unused variable 'vtmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:94: warning: unused variable 'p2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:94: warning: unused variable 'p1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:93: warning: unused variable 'averageaxis' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:87: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:81: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 95 [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_clustsize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_clustsize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_mdmat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_mdmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c: In function 'clust_size': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:97: warning: unused variable 'n_y' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:97: warning: unused variable 'ak' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:92: warning: unused variable 'nsame' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c: In function 'gmx_clustsize': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:407: warning: unused variable 'bRDF' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:407: warning: unused variable 'bSQ' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c: In function 'gmx_mdmat': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c:194: warning: unused variable 'nr0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c:192: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c:165: warning: unused variable 'bAtom' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_wham.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_wham.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_wham.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/correl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/correl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/correl.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_sham.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_sham.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/correl.c: In function 'complex_mult': /builddir/build/BUILD/gromacs-4.5.5/src/tools/correl.c:188: warning: unused variable 'no2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/correl.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c: In function 'do_sham': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:288: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c: In function 'gmx_sham': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'db' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'cum4' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'cum3' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'cum2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'cum1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'sig' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'av' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:776: warning: unused variable 'error' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:776: warning: unused variable 'tot' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:775: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:775: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:775: warning: unused variable 'nlast' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:774: warning: unused variable 'out' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:728: warning: unused variable 'resol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:728: warning: unused variable 'nb_min' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:723: warning: unused variable 'bShamEner' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:722: warning: unused variable 'bPower' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:722: warning: unused variable 'bEeFitAc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:722: warning: unused variable 'bEENLC' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:722: warning: unused variable 'bEESEF' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:721: warning: unused variable 'bXYdy' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:721: warning: unused variable 'bAverCorr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:721: warning: unused variable 'bSubAv' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:720: warning: unused variable 'filtlen' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:720: warning: unused variable 'frac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_nmtraj.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_nmtraj.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c: In function 'gmx_nmtraj': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:124: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:123: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:121: warning: unused variable 'out_eigval' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:115: warning: unused variable 'neigval' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:113: warning: unused variable 'grpname' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:111: warning: unused variable 'indexfile' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:109: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:109: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:105: warning: unused variable 'eigvalnr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_trjconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_trjconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_trjcat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_trjcat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c: In function 'calc_pbc_cluster': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:111: warning: unused variable 'com_dist2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c: In function 'put_molecule_com_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:282: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c: In function 'gmx_trjconv': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:826: warning: unused variable 'xdr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:825: warning: unused variable 'command' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:803: warning: unused variable 'gn_rms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:802: warning: unused variable 'ind_rms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:801: warning: unused variable 'irms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:790: warning: unused variable 'nre' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:789: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:789: warning: unused variable 'xtcpr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:788: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:788: warning: unused variable 'box_center' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:72: warning: 'sort_comdist2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c: In function 'scan_trj_files': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:81: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c: In function 'gmx_trjcat': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:464: warning: unused variable 'last_ok_step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:460: warning: unused variable 'in_file' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:457: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:457: warning: unused variable 'x' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:455: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:455: warning: unused variable 'ftpin' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 96 [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_trjorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_trjorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjorder.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_xpm2ps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_xpm2ps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'xpm_mat': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:570: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:570: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:569: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'tick_spacing': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:610: warning: unused variable 'bFive' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'ps_mat': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:655: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'write_combined_matrix': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:931: warning: unused variable 'map' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'gmx_xpm2ps': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:1146: warning: unused variable 'bAdd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_editconf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_editconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c: In function 'calc_geom': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:109: warning: unused variable 'grpnames' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c: In function 'set_pdb_conf_bfac': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:212: warning: unused variable 'out' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c: In function 'gmx_editconf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'zcent' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'ycent' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'xcent' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'zs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'ys' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'xs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:671: warning: unused variable 'bCubic' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:666: warning: unused variable 'tindex' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:665: warning: unused variable 'tsize' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:563: warning: unused variable 'to_diam' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:563: warning: unused variable 'rbox' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:82: warning: 'pdbtp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_genbox.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_genbox.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genbox.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genbox.c: In function 'gmx_genbox': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genbox.c:694: warning: unused variable 'pbc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genbox.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_genion.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_genion.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c: In function 'insert_ion': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:72: warning: unused variable 'xei' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:70: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:70: warning: unused variable 'wlast' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:70: warning: unused variable 'owater' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c: In function 'update_topol': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:236: warning: unused variable 'nsol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_genconf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_genconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genconf.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genconf.c:93: warning: 'move_x' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_genpr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_genpr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genpr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 97 [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_eneconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_eneconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used[ 87%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/tools/CMakeFiles/gmxana.dir/gmx_vanhove.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_vanhove.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_vanhove.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 87%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c: In function 'scan_ene_files': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:148: warning: unused variable 'i' Building C object src/tools/CMakeFiles/gmxana.dir/gmx_wheel.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_wheel.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_wheel.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c: In function 'gmx_eneconv': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:499: warning: unused variable 'ok' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:498: warning: unused variable 'buf3' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:498: warning: unused variable 'chptr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:498: warning: unused variable 'inputstring' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:497: warning: unused variable 't1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:494: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:102: warning: 'same_time' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:318: warning: 'remove_last_eeframe' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:386: warning: 'update_last_ee' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/addconf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/addconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c: In function 'add_conf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:331: warning: unused variable 'xpp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dz1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dz0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dy1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dy0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dx1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dx0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:328: warning: unused variable 'maxincell' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:328: warning: unused variable 'ncells' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:328: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:327: warning: unused variable 'iprot' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:327: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:327: warning: unused variable 'jj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:325: warning: unused variable 'ib2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:325: warning: unused variable 'ib1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:70: warning: 'set_margin' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/calcpot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/calcpot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c: In function 'c_tabpot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:79: warning: unused variable 'qqO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'rinv2O' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'fsO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'vcO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'tzO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'tyO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'txO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fzO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fyO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fxO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fzJ' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fyJ' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fxJ' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:75: warning: unused variable 'ggid' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:71: warning: unused variable 'FF' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:71: warning: unused variable 'fijC' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:70: warning: unused variable 'two' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c: In function 'init_calcpot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:222: warning: unused variable 'xtc_traj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:222: warning: unused variable 'traj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/edittop.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_bar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_membed.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_membed.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c: In function 'delete_from_block': /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c:103: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c:103: warning: unused variable 'j1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c: In function 'delete_atom': /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c:160: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'barres_list_create': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:758: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'sample_coll_create_subsample': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1024: warning: unused variable 'hist_end' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1024: warning: unused variable 'hist_start' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'calc_bar_lowlevel': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1253: warning: unused variable 'sum2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1253: warning: unused variable 'sum1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1250: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1249: warning: unused variable 'DG' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'calc_bar': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1616: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1614: warning: unused variable 'nsample2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1614: warning: unused variable 'nsample1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'read_bar_xvg': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2041: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'read_edr_rawdh_block': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2087: warning: unused variable 'allocated' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'read_edr_hist_block': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2238: warning: unused variable 'nbin' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'read_barsim_edr': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2286: warning: unused variable 'end_time' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'gmx_bar': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2608: warning: unused variable 'dg_tot_min' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2608: warning: unused variable 'dg_tot_max' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2608: warning: unused variable 'sig' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2608: warning: unused variable 'dg' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2596: warning: unused variable 'nbs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2594: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2594: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2574: warning: unused variable 'calc_v' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2574: warning: unused variable 'calc_s' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:258: warning: 'samples_destroy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c: In function 'do_md_membed': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:1016: warning: unused variable 'bIterate' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:1013: warning: unused variable 'bTCR' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:1010: warning: unused variable 'timestep' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:986: warning: unused variable 'ebox' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:986: warning: unused variable 'scale_tot' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:976: warning: unused variable 'bCPT' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c: In function 'mdrunner_membed': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2749: warning: unused variable 'nthreads_requested' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2749: warning: unused variable 'nthreads' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2748: warning: unused variable 'cr_old' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2743: warning: unused variable 'list' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2740: warning: unused variable 'gro' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2739: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2739: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2729: warning: unused variable 'tmpr2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2729: warning: unused variable 'tmpr1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2723: warning: unused variable 'realtime' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2723: warning: unused variable 'nodetime' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c: In function 'gmx_membed': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3691: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3642: warning: unused variable 'fptest' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3641: warning: unused variable 'HaveCheckpoint' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3637: warning: unused variable 'ed' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3506: warning: unused variable 'bPPPME' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3505: warning: unused variable 'bCart' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 98 /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 88%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used Building C object src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_pme_error.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_pme_error.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_options.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_options.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_options.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dos.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dos.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c: In function 'gmx_dos': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:291: warning: unused variable 'dosabs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:290: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:290: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:288: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:143: warning: 'old_calc_fluidicity' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 88%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/gmxana.dir/gmx_hydorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_hydorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_densorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_densorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c: In function 'calc_tetra_order_interface': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c:280: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c:274: warning: unused variable 'subtitle' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/interf.h:46: warning: 'init_interf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c:64: warning: 'print_types' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c:76: warning: 'check_length' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'density_in_time': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:114: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:114: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'outputfield': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:302: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:311: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'filterdensmap': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:348: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:346: warning: unused variable 'output' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'interfaces_txy': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'spread' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'alpha' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'densr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'densl' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:379: warning: unused variable 'deltandx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'gmx_densorder': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:656: warning: unused variable 'title' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:259: warning: 'printdensavg' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:322: warning: 'periodic_running_average' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/powerspect.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/powerspect.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/powerspect.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/interf.h:46: warning: 'init_interf' defined but not used [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/dens_filter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/dens_filter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 99 [ 89%] Building C object src/tools/CMakeFiles/gmxana.dir/binsearch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/binsearch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/binsearch.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c: In function 'periodic_convolution': /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c:96: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c:96: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Linking C shared library libgmxana.so cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana.dir/link.txt --verbose=1 /usr/bin/gcc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libgmxana.so.6 -o libgmxana.so.6 CMakeFiles/gmxana.dir/autocorr.c.o CMakeFiles/gmxana.dir/expfit.c.o CMakeFiles/gmxana.dir/polynomials.c.o CMakeFiles/gmxana.dir/levenmar.c.o CMakeFiles/gmxana.dir/anadih.c.o CMakeFiles/gmxana.dir/pp2shift.c.o CMakeFiles/gmxana.dir/dlist.c.o CMakeFiles/gmxana.dir/eigio.c.o CMakeFiles/gmxana.dir/cmat.c.o CMakeFiles/gmxana.dir/eigensolver.c.o CMakeFiles/gmxana.dir/nsc.c.o CMakeFiles/gmxana.dir/hxprops.c.o CMakeFiles/gmxana.dir/fitahx.c.o CMakeFiles/gmxana.dir/geminate.c.o CMakeFiles/gmxana.dir/gmx_analyze.c.o CMakeFiles/gmxana.dir/gmx_anaeig.c.o CMakeFiles/gmxana.dir/gmx_angle.c.o CMakeFiles/gmxana.dir/gmx_bond.c.o CMakeFiles/gmxana.dir/gmx_bundle.c.o CMakeFiles/gmxana.dir/gmx_chi.c.o CMakeFiles/gmxana.dir/gmx_cluster.c.o CMakeFiles/gmxana.dir/gmx_confrms.c.o CMakeFiles/gmxana.dir/gmx_covar.c.o CMakeFiles/gmxana.dir/gmx_current.c.o CMakeFiles/gmxana.dir/gmx_density.c.o CMakeFiles/gmxana.dir/gmx_densmap.c.o CMakeFiles/gmxana.dir/gmx_dih.c.o CMakeFiles/gmxana.dir/gmx_dielectric.c.o CMakeFiles/gmxana.dir/gmx_kinetics.c.o CMakeFiles/gmxana.dir/gmx_spatial.c.o CMakeFiles/gmxana.dir/gmx_tune_pme.c.o CMakeFiles/gmxana.dir/gmx_dipoles.c.o CMakeFiles/gmxana.dir/gmx_disre.c.o CMakeFiles/gmxana.dir/gmx_dist.c.o CMakeFiles/gmxana.dir/gmx_dyndom.c.o CMakeFiles/gmxana.dir/gmx_enemat.c.o CMakeFiles/gmxana.dir/gmx_energy.c.o CMakeFiles/gmxana.dir/gmx_lie.c.o CMakeFiles/gmxana.dir/gmx_filter.c.o CMakeFiles/gmxana.dir/gmx_gyrate.c.o CMakeFiles/gmxana.dir/gmx_h2order.c.o CMakeFiles/gmxana.dir/gmx_hbond.c.o CMakeFiles/gmxana.dir/gmx_helix.c.o CMakeFiles/gmxana.dir/gmx_mindist.c.o CMakeFiles/gmxana.dir/gmx_msd.c.o CMakeFiles/gmxana.dir/gmx_morph.c.o CMakeFiles/gmxana.dir/gmx_nmeig.c.o CMakeFiles/gmxana.dir/gmx_nmens.c.o CMakeFiles/gmxana.dir/gmx_order.c.o CMakeFiles/gmxana.dir/gmx_principal.c.o CMakeFiles/gmxana.dir/gmx_polystat.c.o CMakeFiles/gmxana.dir/gmx_potential.c.o CMakeFiles/gmxana.dir/gmx_rama.c.o CMakeFiles/gmxana.dir/gmx_rdf.c.o CMakeFiles/gmxana.dir/gmx_rms.c.o CMakeFiles/gmxana.dir/gmx_rmsf.c.o CMakeFiles/gmxana.dir/gmx_rotacf.c.o CMakeFiles/gmxana.dir/gmx_saltbr.c.o CMakeFiles/gmxana.dir/gmx_sas.c.o CMakeFiles/gmxana.dir/gmx_select.c.o CMakeFiles/gmxana.dir/gmx_rmsdist.c.o CMakeFiles/gmxana.dir/gmx_rotmat.c.o CMakeFiles/gmxana.dir/gmx_sgangle.c.o CMakeFiles/gmxana.dir/gmx_sorient.c.o CMakeFiles/gmxana.dir/gmx_spol.c.o CMakeFiles/gmxana.dir/gmx_tcaf.c.o CMakeFiles/gmxana.dir/gmx_traj.c.o CMakeFiles/gmxana.dir/gmx_velacc.c.o CMakeFiles/gmxana.dir/gmx_helixorient.c.o CMakeFiles/gmxana.dir/gmx_clustsize.c.o CMakeFiles/gmxana.dir/gmx_mdmat.c.o CMakeFiles/gmxana.dir/gmx_wham.c.o CMakeFiles/gmxana.dir/correl.c.o CMakeFiles/gmxana.dir/gmx_sham.c.o CMakeFiles/gmxana.dir/gmx_nmtraj.c.o CMakeFiles/gmxana.dir/gmx_trjconv.c.o CMakeFiles/gmxana.dir/gmx_trjcat.c.o CMakeFiles/gmxana.dir/gmx_trjorder.c.o CMakeFiles/gmxana.dir/gmx_xpm2ps.c.o CMakeFiles/gmxana.dir/gmx_editconf.c.o CMakeFiles/gmxana.dir/gmx_genbox.c.o CMakeFiles/gmxana.dir/gmx_genion.c.o CMakeFiles/gmxana.dir/gmx_genconf.c.o CMakeFiles/gmxana.dir/gmx_genpr.c.o CMakeFiles/gmxana.dir/gmx_eneconv.c.o CMakeFiles/gmxana.dir/gmx_vanhove.c.o CMakeFiles/gmxana.dir/gmx_wheel.c.o CMakeFiles/gmxana.dir/addconf.c.o CMakeFiles/gmxana.dir/calcpot.c.o CMakeFiles/gmxana.dir/edittop.c.o CMakeFiles/gmxana.dir/gmx_bar.c.o CMakeFiles/gmxana.dir/gmx_membed.c.o CMakeFiles/gmxana.dir/gmx_pme_error.c.o CMakeFiles/gmxana.dir/gmx_options.c.o CMakeFiles/gmxana.dir/gmx_dos.c.o CMakeFiles/gmxana.dir/gmx_hydorder.c.o CMakeFiles/gmxana.dir/gmx_densorder.c.o CMakeFiles/gmxana.dir/powerspect.c.o CMakeFiles/gmxana.dir/dens_filter.c.o CMakeFiles/gmxana.dir/binsearch.c.o ../mdlib/libmd.so.6 ../gmxlib/libgmx.so.6 -lpthread -ldl -lm -lfftw3f -lxml2 cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_symlink_library libgmxana.so.6 libgmxana.so.6 libgmxana.so make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 86 87 88 89 90 91 92 93 94 95 96 97 98 99 [ 89%] Built target gmxana make -f src/tools/CMakeFiles/do_dssp.dir/build.make src/tools/CMakeFiles/do_dssp.dir/depend make -f src/tools/CMakeFiles/editconf.dir/build.make src/tools/CMakeFiles/editconf.dir/depend make -f src/tools/CMakeFiles/eneconv.dir/build.make src/tools/CMakeFiles/eneconv.dir/depend make -f src/tools/CMakeFiles/g_anadock.dir/build.make src/tools/CMakeFiles/g_anadock.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/do_dssp.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/editconf.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/eneconv.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_anadock.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/do_dssp.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/do_dssp.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/editconf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/editconf.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_anadock.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_anadock.dir/depend.internal". Scanning dependencies of target editconf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/editconf.dir/build.make src/tools/CMakeFiles/editconf.dir/build Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/eneconv.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/eneconv.dir/depend.internal". Scanning dependencies of target eneconv make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/eneconv.dir/build.make src/tools/CMakeFiles/eneconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] [ 89%] Scanning dependencies of target g_anadock Scanning dependencies of target do_dssp make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/do_dssp.dir/build.make src/tools/CMakeFiles/do_dssp.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_anadock.dir/build.make src/tools/CMakeFiles/g_anadock.dir/build Building C object src/tools/CMakeFiles/editconf.dir/editconf.c.o Building C object src/tools/CMakeFiles/eneconv.dir/eneconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/editconf.dir/editconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/editconf.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/eneconv.dir/eneconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/eneconv.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] [ 89%] Building C object src/tools/CMakeFiles/g_anadock.dir/g_anadock.c.o Building C object src/tools/CMakeFiles/do_dssp.dir/do_dssp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/do_dssp.dir/do_dssp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/do_dssp.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_anadock.dir/g_anadock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_anadock.c Linking C executable eneconv cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/eneconv.dir/link.txt --verbose=1 Linking C executable editconf cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/editconf.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/editconf.dir/editconf.c.o -o editconf -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/eneconv.dir/eneconv.c.o -o eneconv -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] Built target editconf make -f src/tools/CMakeFiles/g_anaeig.dir/build.make src/tools/CMakeFiles/g_anaeig.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 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/builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] Built target eneconv make -f src/tools/CMakeFiles/g_analyze.dir/build.make src/tools/CMakeFiles/g_analyze.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_anaeig.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_anaeig.dir/depend.internal". Scanning dependencies of target g_anaeig make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_anaeig.dir/build.make src/tools/CMakeFiles/g_anaeig.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_analyze.dir/DependInfo.cmake --color= /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_analyze.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_analyze.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report 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defined but not used [ 89%] [ 89%] Building C object src/tools/CMakeFiles/g_anaeig.dir/g_anaeig.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_anaeig.dir/g_anaeig.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_anaeig.c Building C object src/tools/CMakeFiles/g_analyze.dir/g_analyze.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_analyze.dir/g_analyze.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_analyze.c Linking C executable g_anaeig cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_anaeig.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_anaeig.dir/g_anaeig.c.o -o g_anaeig -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_analyze cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_analyze.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_analyze.dir/g_analyze.c.o -o g_analyze 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Scanning dependencies of target g_angle make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_angle.dir/build.make src/tools/CMakeFiles/g_angle.dir/build [ 89%] Built target g_analyze make -f src/tools/CMakeFiles/g_bar.dir/build.make src/tools/CMakeFiles/g_bar.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 76 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bar.dir/DependInfo.cmake --color= [ 90%] Building C object src/tools/CMakeFiles/g_angle.dir/g_angle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_angle.dir/g_angle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_angle.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bar.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bar.dir/depend.internal". Scanning dependencies of target g_bar make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_bar.dir/build.make src/tools/CMakeFiles/g_bar.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Building C object src/tools/CMakeFiles/g_bar.dir/g_bar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_bar.dir/g_bar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_bar.c Linking C executable g_angle cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_angle.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_angle.dir/g_angle.c.o -o g_angle -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_bar cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_bar.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_bar.dir/g_bar.c.o -o g_bar -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_anadock cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_anadock.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 76 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_anadock.dir/g_anadock.c.o -o g_anadock -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 90%] Built target g_angle make -f src/tools/CMakeFiles/g_bond.dir/build.make src/tools/CMakeFiles/g_bond.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bond.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bond.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bond.dir/depend.internal". Scanning dependencies of target g_bond make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_bond.dir/build.make src/tools/CMakeFiles/g_bond.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Building C object src/tools/CMakeFiles/g_bond.dir/g_bond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_bond.dir/g_bond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_bond.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Built target g_bar make -f src/tools/CMakeFiles/g_bundle.dir/build.make src/tools/CMakeFiles/g_bundle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bundle.dir/DependInfo.cmake --color= Linking C executable g_bond cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_bond.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bundle.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bundle.dir/depend.internal". /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_bond.dir/g_bond.c.o -o g_bond -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 90%] Built target g_anadock Scanning dependencies of target g_bundle make -f src/tools/CMakeFiles/g_chi.dir/build.make src/tools/CMakeFiles/g_chi.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_bundle.dir/build.make src/tools/CMakeFiles/g_bundle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_chi.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_chi.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_chi.dir/depend.internal". Scanning dependencies of target g_chi make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_chi.dir/build.make src/tools/CMakeFiles/g_chi.dir/build Building C object src/tools/CMakeFiles/g_bundle.dir/g_bundle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_bundle.dir/g_bundle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_bundle.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Building C object src/tools/CMakeFiles/g_chi.dir/g_chi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_chi.dir/g_chi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_chi.c Linking C executable g_bundle cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_bundle.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_bundle.dir/g_bundle.c.o -o g_bundle -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_chi cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_chi.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_chi.dir/g_chi.c.o -o g_chi -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 90%] Built target g_bond make -f src/tools/CMakeFiles/g_cluster.dir/build.make src/tools/CMakeFiles/g_cluster.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_cluster.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_cluster.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_cluster.dir/depend.internal". Scanning dependencies of target g_cluster make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_cluster.dir/build.make src/tools/CMakeFiles/g_cluster.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Building C object src/tools/CMakeFiles/g_cluster.dir/g_cluster.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_cluster.dir/g_cluster.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_cluster.c [ 90%] Built target g_bundle make -f src/tools/CMakeFiles/g_clustsize.dir/build.make src/tools/CMakeFiles/g_clustsize.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_clustsize.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Built target g_chi make -f src/tools/CMakeFiles/g_confrms.dir/build.make src/tools/CMakeFiles/g_confrms.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_confrms.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_clustsize.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_clustsize.dir/depend.internal". Scanning dependencies of target g_clustsize make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_clustsize.dir/build.make src/tools/CMakeFiles/g_clustsize.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Linking C executable g_cluster cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_cluster.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_confrms.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_confrms.dir/depend.internal". [ 90%] Scanning dependencies of target g_confrms /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_cluster.dir/g_cluster.c.o -o g_cluster -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_confrms.dir/build.make src/tools/CMakeFiles/g_confrms.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 77 Building C object src/tools/CMakeFiles/g_clustsize.dir/g_clustsize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_clustsize.dir/g_clustsize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_clustsize.c Linking C executable do_dssp [ 91%] cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/do_dssp.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/do_dssp.dir/do_dssp.c.o -o do_dssp -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_confrms.dir/g_confrms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_confrms.dir/g_confrms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_confrms.c Linking C executable g_clustsize cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_clustsize.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_clustsize.dir/g_clustsize.c.o -o g_clustsize -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_confrms cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_confrms.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_confrms.dir/g_confrms.c.o -o g_confrms -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_cluster make -f src/tools/CMakeFiles/g_covar.dir/build.make src/tools/CMakeFiles/g_covar.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 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Scanning dependencies of target g_covar make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_covar.dir/build.make src/tools/CMakeFiles/g_covar.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_current.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_current.dir/depend.internal". [ 91%] Scanning dependencies of target g_current [ 91%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_current.dir/build.make src/tools/CMakeFiles/g_current.dir/build Built target g_clustsize make -f src/tools/CMakeFiles/g_density.dir/build.make src/tools/CMakeFiles/g_density.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_density.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_covar.dir/g_covar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_covar.dir/g_covar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_covar.c [ 91%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 77 Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_density.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_density.dir/depend.internal". Building C object src/tools/CMakeFiles/g_current.dir/g_current.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_current.dir/g_current.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_current.c Scanning dependencies of target g_density make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_density.dir/build.make src/tools/CMakeFiles/g_density.dir/build [ 91%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Built target g_confrms make -f src/tools/CMakeFiles/g_densmap.dir/build.make 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/builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_density.dir/g_density.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_density.c Scanning dependencies of target g_densmap make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_densmap.dir/build.make src/tools/CMakeFiles/g_densmap.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_covar.dir/g_covar.c.o -o g_covar -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_current cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_current.dir/link.txt --verbose=1 [ 91%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_current.dir/g_current.c.o -o g_current -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_densmap.dir/g_densmap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_densmap.dir/g_densmap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_densmap.c Linking C executable g_density cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_density.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_density.dir/g_density.c.o -o g_density -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_densmap cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_densmap.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_densmap.dir/g_densmap.c.o -o g_densmap -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_covar make -f src/tools/CMakeFiles/g_densorder.dir/build.make src/tools/CMakeFiles/g_densorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_densorder.dir/DependInfo.cmake --color= make[2]: 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Scanning dependencies of target g_densorder make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_densorder.dir/build.make src/tools/CMakeFiles/g_densorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dielectric.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dielectric.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dielectric.dir/depend.internal". Building C object src/tools/CMakeFiles/g_densorder.dir/g_densorder.c.o Scanning dependencies of target g_dielectric cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_densorder.dir/g_densorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_densorder.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dielectric.dir/build.make src/tools/CMakeFiles/g_dielectric.dir/build /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] [ 91%] Built target g_densmap Built target g_current make -f src/tools/CMakeFiles/g_dih.dir/build.make src/tools/CMakeFiles/g_dih.dir/depend make -f src/tools/CMakeFiles/g_dipoles.dir/build.make src/tools/CMakeFiles/g_dipoles.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dih.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dipoles.dir/DependInfo.cmake --color= [ 91%] Building C object src/tools/CMakeFiles/g_dielectric.dir/g_dielectric.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dielectric.dir/g_dielectric.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dielectric.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dipoles.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dipoles.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dih.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dih.dir/depend.internal". Scanning dependencies of target g_dih Scanning dependencies of target g_dipoles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' Linking C executable g_densorder make -f src/tools/CMakeFiles/g_dih.dir/build.make src/tools/CMakeFiles/g_dih.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dipoles.dir/build.make src/tools/CMakeFiles/g_dipoles.dir/build cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_densorder.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 78 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_densorder.dir/g_densorder.c.o -o g_densorder -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 92%] [ 92%] Building C object src/tools/CMakeFiles/g_dipoles.dir/g_dipoles.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dipoles.dir/g_dipoles.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dipoles.c Building C object src/tools/CMakeFiles/g_dih.dir/g_dih.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dih.dir/g_dih.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dih.c Linking C executable g_dielectric cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dielectric.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dielectric.dir/g_dielectric.c.o -o g_dielectric -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_dipoles Linking C executable g_dih cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dipoles.dir/link.txt --verbose=1 cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dih.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dih.dir/g_dih.c.o -o g_dih -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dipoles.dir/g_dipoles.c.o -o g_dipoles -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report 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"/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_disre.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_disre.dir/depend.internal". /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dist.dir/DependInfo.cmake --color= Scanning dependencies of target g_disre make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_disre.dir/build.make src/tools/CMakeFiles/g_disre.dir/build [ 92%] Built target g_dih make -f 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Building C object src/tools/CMakeFiles/g_disre.dir/g_disre.c.o Built target g_dipoles make -f src/tools/CMakeFiles/g_dyndom.dir/build.make src/tools/CMakeFiles/g_dyndom.dir/depend cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_disre.dir/g_disre.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_disre.c Scanning dependencies of target g_dos make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dos.dir/build.make src/tools/CMakeFiles/g_dos.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dyndom.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' [ 92%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] Building C object src/tools/CMakeFiles/g_dist.dir/g_dist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dist.dir/g_dist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dist.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dyndom.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dyndom.dir/depend.internal". Scanning dependencies of target g_dyndom make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dyndom.dir/build.make src/tools/CMakeFiles/g_dyndom.dir/build Building C object src/tools/CMakeFiles/g_dos.dir/g_dos.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dos.dir/g_dos.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dos.c Linking C executable g_disre cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_disre.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report 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/usr/bin/cmake -E cmake_link_script CMakeFiles/g_dist.dir/link.txt --verbose=1 Linking C executable g_dos cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dos.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dist.dir/g_dist.c.o -o g_dist -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dos.dir/g_dos.c.o -o g_dos -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_dyndom cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dyndom.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dyndom.dir/g_dyndom.c.o -o g_dyndom -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] Built target g_disre make -f src/tools/CMakeFiles/g_enemat.dir/build.make src/tools/CMakeFiles/g_enemat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single 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Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_filter.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_filter.dir/depend.internal". Scanning dependencies of target g_energy make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_energy.dir/build.make src/tools/CMakeFiles/g_energy.dir/build Scanning dependencies of target g_filter make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_filter.dir/build.make src/tools/CMakeFiles/g_filter.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 79 Linking C executable g_enemat Building C object src/tools/CMakeFiles/g_energy.dir/g_energy.c.o [ 92%] cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_energy.dir/g_energy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_energy.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_enemat.dir/link.txt --verbose=1 Built target g_dyndom make -f src/tools/CMakeFiles/g_gyrate.dir/build.make src/tools/CMakeFiles/g_gyrate.dir/depend [ 93%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_gyrate.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_enemat.dir/g_enemat.c.o -o g_enemat -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_filter.dir/g_filter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_filter.dir/g_filter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_filter.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_gyrate.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_gyrate.dir/depend.internal". Scanning dependencies of target g_gyrate make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_gyrate.dir/build.make src/tools/CMakeFiles/g_gyrate.dir/build Linking C executable g_energy cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_energy.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_energy.dir/g_energy.c.o -o g_energy -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_filter cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_filter.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_gyrate.dir/g_gyrate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_gyrate.dir/g_gyrate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_gyrate.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_filter.dir/g_filter.c.o -o g_filter -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_gyrate cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_gyrate.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_gyrate.dir/g_gyrate.c.o -o g_gyrate -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_enemat make -f src/tools/CMakeFiles/g_h2order.dir/build.make src/tools/CMakeFiles/g_h2order.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single 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-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_h2order.dir/g_h2order.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_h2order.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_helix.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_hbond.dir/DependInfo.cmake" is newer than depender 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Linking C executable g_h2order cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_h2order.dir/link.txt --verbose=1 Scanning dependencies of target g_helixorient make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_helixorient.dir/build.make src/tools/CMakeFiles/g_helixorient.dir/build Building C object src/tools/CMakeFiles/g_helix.dir/g_helix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_helix.dir/g_helix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_helix.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_h2order.dir/g_h2order.c.o -o g_h2order -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 93%] Building C object src/tools/CMakeFiles/g_helixorient.dir/g_helixorient.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_helixorient.dir/g_helixorient.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_helixorient.c Linking C executable g_hbond cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_hbond.dir/link.txt --verbose=1 Linking C executable g_helix /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_hbond.dir/g_hbond.c.o -o g_hbond -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_helix.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_helix.dir/g_helix.c.o -o g_helix -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_helixorient cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_helixorient.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_helixorient.dir/g_helixorient.c.o -o g_helixorient -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_h2order make -f src/tools/CMakeFiles/g_hydorder.dir/build.make src/tools/CMakeFiles/g_hydorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_hydorder.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] [ 93%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_hydorder.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_hydorder.dir/depend.internal". Built target g_hbond make -f src/tools/CMakeFiles/g_kinetics.dir/build.make src/tools/CMakeFiles/g_kinetics.dir/depend Built target g_helix make -f src/tools/CMakeFiles/g_lie.dir/build.make src/tools/CMakeFiles/g_lie.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_kinetics.dir/DependInfo.cmake --color= Scanning dependencies of target g_hydorder make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_lie.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_hydorder.dir/build.make src/tools/CMakeFiles/g_hydorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_lie.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_lie.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_kinetics.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_kinetics.dir/depend.internal". Scanning dependencies of target g_lie make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_lie.dir/build.make src/tools/CMakeFiles/g_lie.dir/build [ 93%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' Scanning dependencies of target g_kinetics /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 80 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_kinetics.dir/build.make src/tools/CMakeFiles/g_kinetics.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Building C object src/tools/CMakeFiles/g_hydorder.dir/g_hydorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_hydorder.dir/g_hydorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_hydorder.c [ 94%] Building C object src/tools/CMakeFiles/g_lie.dir/g_lie.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_lie.dir/g_lie.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_lie.c Building C object src/tools/CMakeFiles/g_kinetics.dir/g_kinetics.c.o make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_kinetics.dir/g_kinetics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_kinetics.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Built target g_helixorient make -f src/tools/CMakeFiles/g_mdmat.dir/build.make src/tools/CMakeFiles/g_mdmat.dir/depend Linking C executable g_hydorder cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_hydorder.dir/link.txt --verbose=1 Linking C executable g_lie cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_lie.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_mdmat.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_hydorder.dir/g_hydorder.c.o -o g_hydorder -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_lie.dir/g_lie.c.o -o g_lie -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_mdmat.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_mdmat.dir/depend.internal". Linking C executable g_kinetics cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_kinetics.dir/link.txt --verbose=1 Scanning dependencies of target g_mdmat make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_mdmat.dir/build.make src/tools/CMakeFiles/g_mdmat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_kinetics.dir/g_kinetics.c.o -o g_kinetics -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_mdmat.dir/g_mdmat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_mdmat.dir/g_mdmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_mdmat.c Linking C executable g_mdmat cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_mdmat.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_mdmat.dir/g_mdmat.c.o -o g_mdmat -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 80 Built target g_hydorder make -f src/tools/CMakeFiles/g_membed.dir/build.make src/tools/CMakeFiles/g_membed.dir/depend [ 94%] Built target g_lie make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_membed.dir/DependInfo.cmake --color= make -f src/tools/CMakeFiles/g_mindist.dir/build.make src/tools/CMakeFiles/g_mindist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_mindist.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_mindist.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_mindist.dir/depend.internal". make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Scanning dependencies of target g_mindist make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_mindist.dir/build.make src/tools/CMakeFiles/g_mindist.dir/build [ 94%] Built target g_kinetics make -f src/tools/CMakeFiles/g_morph.dir/build.make src/tools/CMakeFiles/g_morph.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_morph.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_membed.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_membed.dir/depend.internal". [ 94%] Scanning dependencies of target g_membed make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_membed.dir/build.make src/tools/CMakeFiles/g_membed.dir/build Building C object src/tools/CMakeFiles/g_mindist.dir/g_mindist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_mindist.dir/g_mindist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_mindist.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_morph.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_morph.dir/depend.internal". Scanning dependencies of target g_morph make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_morph.dir/build.make src/tools/CMakeFiles/g_morph.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] [ 94%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/g_membed.dir/g_membed.c.o Building C object src/tools/CMakeFiles/g_morph.dir/g_morph.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_morph.dir/g_morph.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_morph.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_membed.dir/g_membed.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_membed.c [ 94%] Built target g_mdmat make -f src/tools/CMakeFiles/g_msd.dir/build.make src/tools/CMakeFiles/g_msd.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_msd.dir/DependInfo.cmake --color= Linking C executable g_mindist cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_mindist.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_mindist.dir/g_mindist.c.o -o g_mindist -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_msd.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_msd.dir/depend.internal". Scanning dependencies of target g_msd Linking C executable g_membed make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_msd.dir/build.make src/tools/CMakeFiles/g_msd.dir/build cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_membed.dir/link.txt --verbose=1 Linking C executable g_morph cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_morph.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_morph.dir/g_morph.c.o -o g_morph -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_membed.dir/g_membed.c.o -o g_membed -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 94%] Building C object src/tools/CMakeFiles/g_msd.dir/g_msd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_msd.dir/g_msd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_msd.c Linking C executable g_msd cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_msd.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_msd.dir/g_msd.c.o -o g_msd -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Built target g_mindist make -f src/tools/CMakeFiles/g_nmeig.dir/build.make src/tools/CMakeFiles/g_nmeig.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' [ 94%] cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_nmeig.dir/DependInfo.cmake --color= Built target g_morph make -f src/tools/CMakeFiles/g_nmens.dir/build.make src/tools/CMakeFiles/g_nmens.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_nmens.dir/DependInfo.cmake --color= [ 94%] Built target g_membed make -f src/tools/CMakeFiles/g_nmtraj.dir/build.make src/tools/CMakeFiles/g_nmtraj.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_nmtraj.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_nmeig.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_nmeig.dir/depend.internal". 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Scanning dependencies of target g_options Linking C executable g_nmens /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_nmeig.dir/g_nmeig.c.o -o g_nmeig -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_nmens.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_options.dir/build.make src/tools/CMakeFiles/g_options.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Linking C executable g_nmtraj cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_nmtraj.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_nmens.dir/g_nmens.c.o -o g_nmens -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 95%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_nmtraj.dir/g_nmtraj.c.o -o g_nmtraj -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_options.dir/g_options.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_options.dir/g_options.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_options.c Linking C executable g_options cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_options.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_options.dir/g_options.c.o -o g_options -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 81 Built target g_nmeig make -f src/tools/CMakeFiles/g_order.dir/build.make src/tools/CMakeFiles/g_order.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_order.dir/DependInfo.cmake --color= [ 95%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Built target g_nmens make -f src/tools/CMakeFiles/g_pme_error.dir/build.make src/tools/CMakeFiles/g_pme_error.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_pme_error.dir/DependInfo.cmake --color= [ 95%] Built target g_nmtraj make -f src/tools/CMakeFiles/g_polystat.dir/build.make src/tools/CMakeFiles/g_polystat.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_order.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_order.dir/depend.internal". 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[ 95%] [ 95%] Scanning dependencies of target g_polystat make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_polystat.dir/build.make src/tools/CMakeFiles/g_polystat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/g_pme_error.dir/g_pme_error.c.o Building C object src/tools/CMakeFiles/g_order.dir/g_order.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_order.dir/g_order.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_order.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_pme_error.dir/g_pme_error.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_pme_error.c [ 95%] Building C object src/tools/CMakeFiles/g_polystat.dir/g_polystat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_polystat.dir/g_polystat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_polystat.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_options make -f src/tools/CMakeFiles/g_potential.dir/build.make src/tools/CMakeFiles/g_potential.dir/depend Linking C executable g_pme_error make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_potential.dir/DependInfo.cmake --color= cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_pme_error.dir/link.txt --verbose=1 Linking C executable g_order Linking C executable g_polystat /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_pme_error.dir/g_pme_error.c.o -o g_pme_error -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_order.dir/link.txt --verbose=1 cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_polystat.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_potential.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_potential.dir/depend.internal". Scanning dependencies of target g_potential /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_polystat.dir/g_polystat.c.o -o g_polystat -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_order.dir/g_order.c.o -o g_order -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_potential.dir/build.make src/tools/CMakeFiles/g_potential.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Building C object src/tools/CMakeFiles/g_potential.dir/g_potential.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_potential.dir/g_potential.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_potential.c Linking C executable g_potential cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_potential.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_potential.dir/g_potential.c.o -o g_potential -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_pme_error make -f src/tools/CMakeFiles/g_principal.dir/build.make src/tools/CMakeFiles/g_principal.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_principal.dir/DependInfo.cmake --color= [ 95%] Built target g_order make -f src/tools/CMakeFiles/g_rama.dir/build.make src/tools/CMakeFiles/g_rama.dir/depend [ 95%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rama.dir/DependInfo.cmake --color= Built target g_polystat make -f src/tools/CMakeFiles/g_rdf.dir/build.make src/tools/CMakeFiles/g_rdf.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_principal.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_principal.dir/depend.internal". 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Scanning dependencies of target g_rama make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rama.dir/build.make src/tools/CMakeFiles/g_rama.dir/build [ 95%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 82 Building C object src/tools/CMakeFiles/g_principal.dir/g_principal.c.o [ 96%] cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_principal.dir/g_principal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_principal.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rdf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rdf.dir/depend.internal". Scanning dependencies of target g_rdf Building C object src/tools/CMakeFiles/g_rama.dir/g_rama.c.o make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rdf.dir/build.make src/tools/CMakeFiles/g_rdf.dir/build cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rama.dir/g_rama.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rama.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Building C object src/tools/CMakeFiles/g_rdf.dir/g_rdf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rdf.dir/g_rdf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rdf.c Linking C executable g_principal cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_principal.dir/link.txt --verbose=1 Built target g_potential make -f src/tools/CMakeFiles/g_rms.dir/build.make src/tools/CMakeFiles/g_rms.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rms.dir/DependInfo.cmake --color= Linking C executable g_rama cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rama.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_principal.dir/g_principal.c.o -o g_principal -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rama.dir/g_rama.c.o -o g_rama -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rms.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rms.dir/depend.internal". Scanning dependencies of target g_rms make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rms.dir/build.make src/tools/CMakeFiles/g_rms.dir/build Linking C executable g_rdf make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rdf.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rdf.dir/g_rdf.c.o -o g_rdf -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 96%] Building C object src/tools/CMakeFiles/g_rms.dir/g_rms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rms.dir/g_rms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rms.c Linking C executable g_rms cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rms.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rms.dir/g_rms.c.o -o g_rms -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 82 [ 96%] Built target g_principal make -f src/tools/CMakeFiles/g_rmsdist.dir/build.make src/tools/CMakeFiles/g_rmsdist.dir/depend [ 96%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rmsdist.dir/DependInfo.cmake --color= Built target g_rama make -f src/tools/CMakeFiles/g_rmsf.dir/build.make src/tools/CMakeFiles/g_rmsf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rmsf.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rmsf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rmsf.dir/depend.internal". make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rmsdist.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rmsdist.dir/depend.internal". Scanning dependencies of target g_rmsf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rmsf.dir/build.make src/tools/CMakeFiles/g_rmsf.dir/build Scanning dependencies of target g_rmsdist make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rmsdist.dir/build.make src/tools/CMakeFiles/g_rmsdist.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' [ 96%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Built target g_rdf make -f src/tools/CMakeFiles/g_rotacf.dir/build.make src/tools/CMakeFiles/g_rotacf.dir/depend [ 96%] [ 96%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rotacf.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_rmsf.dir/g_rmsf.c.o Building C object src/tools/CMakeFiles/g_rmsdist.dir/g_rmsdist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rmsdist.dir/g_rmsdist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rmsdist.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rmsf.dir/g_rmsf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rmsf.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rotacf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rotacf.dir/depend.internal". Scanning dependencies of target g_rotacf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rotacf.dir/build.make src/tools/CMakeFiles/g_rotacf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Linking C executable g_rmsf cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rmsf.dir/link.txt --verbose=1 Linking C executable g_rmsdist cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rmsdist.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_rotacf.dir/g_rotacf.c.o /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rmsdist.dir/g_rmsdist.c.o -o g_rmsdist -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rotacf.dir/g_rotacf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rotacf.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rmsf.dir/g_rmsf.c.o -o g_rmsf -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 96%] Built target g_rms make -f src/tools/CMakeFiles/g_rotmat.dir/build.make src/tools/CMakeFiles/g_rotmat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rotmat.dir/DependInfo.cmake --color= Linking C executable g_rotacf cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rotacf.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rotmat.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rotmat.dir/depend.internal". Scanning dependencies of target g_rotmat make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rotmat.dir/build.make src/tools/CMakeFiles/g_rotmat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rotacf.dir/g_rotacf.c.o -o g_rotacf -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 96%] Building C object src/tools/CMakeFiles/g_rotmat.dir/g_rotmat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rotmat.dir/g_rotmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rotmat.c Linking C executable g_rotmat cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rotmat.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rotmat.dir/g_rotmat.c.o -o g_rotmat -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 96%] Built target g_rmsdist make -f src/tools/CMakeFiles/g_saltbr.dir/build.make src/tools/CMakeFiles/g_saltbr.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_saltbr.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Built target g_rmsf make -f src/tools/CMakeFiles/g_sas.dir/build.make src/tools/CMakeFiles/g_sas.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_saltbr.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_saltbr.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sas.dir/DependInfo.cmake --color= Scanning dependencies of target g_saltbr make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_saltbr.dir/build.make src/tools/CMakeFiles/g_saltbr.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 83 [ 97%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sas.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sas.dir/depend.internal". Building C object src/tools/CMakeFiles/g_saltbr.dir/g_saltbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_saltbr.dir/g_saltbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_saltbr.c Scanning dependencies of target g_sas make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sas.dir/build.make src/tools/CMakeFiles/g_sas.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] Built target g_rotacf make -f src/tools/CMakeFiles/g_select.dir/build.make src/tools/CMakeFiles/g_select.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' [ 97%] cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_select.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_sas.dir/g_sas.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sas.dir/g_sas.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sas.c Linking C executable g_saltbr cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_saltbr.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_select.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_select.dir/depend.internal". Scanning dependencies of target g_select make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_select.dir/build.make src/tools/CMakeFiles/g_select.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_saltbr.dir/g_saltbr.c.o -o g_saltbr -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_sas cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sas.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/g_select.dir/g_select.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_select.dir/g_select.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_select.c [ 97%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sas.dir/g_sas.c.o -o g_sas -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Built target g_rotmat make -f src/tools/CMakeFiles/g_sgangle.dir/build.make src/tools/CMakeFiles/g_sgangle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sgangle.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sgangle.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sgangle.dir/depend.internal". Scanning dependencies of target g_sgangle make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sgangle.dir/build.make src/tools/CMakeFiles/g_sgangle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Linking C executable g_select cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_select.dir/link.txt --verbose=1 [ 97%] Building C object src/tools/CMakeFiles/g_sgangle.dir/g_sgangle.c.o /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_select.dir/g_select.c.o -o g_select -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sgangle.dir/g_sgangle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sgangle.c Linking C executable g_sgangle cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sgangle.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sgangle.dir/g_sgangle.c.o -o g_sgangle -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 83 [ 97%] Built target g_saltbr make -f src/tools/CMakeFiles/g_sham.dir/build.make src/tools/CMakeFiles/g_sham.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sham.dir/DependInfo.cmake --color= [ 97%] Built target g_sas make -f src/tools/CMakeFiles/g_sigeps.dir/build.make src/tools/CMakeFiles/g_sigeps.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sham.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sham.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sigeps.dir/DependInfo.cmake --color= Scanning dependencies of target g_sham make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sham.dir/build.make src/tools/CMakeFiles/g_sham.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sigeps.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sigeps.dir/depend.internal". [ 97%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/g_sham.dir/g_sham.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sham.dir/g_sham.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sham.c [ 97%] Built target g_select make -f src/tools/CMakeFiles/g_sorient.dir/build.make src/tools/CMakeFiles/g_sorient.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sorient.dir/DependInfo.cmake --color= Scanning dependencies of target g_sigeps make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sigeps.dir/build.make src/tools/CMakeFiles/g_sigeps.dir/build Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sorient.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sorient.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Scanning dependencies of target g_sorient make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sorient.dir/build.make src/tools/CMakeFiles/g_sorient.dir/build [ 97%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/g_sigeps.dir/g_sigeps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sigeps.dir/g_sigeps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sigeps.c Linking C executable g_sham cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sham.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] [ 97%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sham.dir/g_sham.c.o -o g_sham -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Built target g_sgangle make -f src/tools/CMakeFiles/g_spatial.dir/build.make src/tools/CMakeFiles/g_spatial.dir/depend Building C object src/tools/CMakeFiles/g_sorient.dir/g_sorient.c.o make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_spatial.dir/DependInfo.cmake --color= cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sorient.dir/g_sorient.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sorient.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_spatial.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_spatial.dir/depend.internal". Scanning dependencies of target g_spatial make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_spatial.dir/build.make src/tools/CMakeFiles/g_spatial.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 84 [ 98%] Linking C executable g_sorient cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sorient.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_spatial.dir/g_spatial.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_spatial.dir/g_spatial.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_spatial.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sorient.dir/g_sorient.c.o -o g_sorient -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_spatial cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_spatial.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_spatial.dir/g_spatial.c.o -o g_spatial -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_sham make -f src/tools/CMakeFiles/g_spol.dir/build.make src/tools/CMakeFiles/g_spol.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_spol.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_spol.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_spol.dir/depend.internal". /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sigeps.c: In function 'main': Scanning dependencies of target g_spol /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sigeps.c:106: warning: unused variable 'pp' make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_spol.dir/build.make src/tools/CMakeFiles/g_spol.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sigeps.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 98%] Building C object src/tools/CMakeFiles/g_spol.dir/g_spol.c.o make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_spol.dir/g_spol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_spol.c [ 98%] Built target g_sorient make -f src/tools/CMakeFiles/g_tcaf.dir/build.make src/tools/CMakeFiles/g_tcaf.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 84 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_tcaf.dir/DependInfo.cmake --color= [ 98%] Built target g_spatial Linking C executable g_spol make -f src/tools/CMakeFiles/g_traj.dir/build.make src/tools/CMakeFiles/g_traj.dir/depend cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_spol.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_tcaf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_tcaf.dir/depend.internal". Scanning dependencies of target g_tcaf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_tcaf.dir/build.make src/tools/CMakeFiles/g_tcaf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_traj.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_spol.dir/g_spol.c.o -o g_spol -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_traj.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_traj.dir/depend.internal". Scanning dependencies of target g_traj make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_traj.dir/build.make src/tools/CMakeFiles/g_traj.dir/build Building C object src/tools/CMakeFiles/g_tcaf.dir/g_tcaf.c.o make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_tcaf.dir/g_tcaf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_tcaf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Building C object src/tools/CMakeFiles/g_traj.dir/g_traj.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_traj.dir/g_traj.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_traj.c Linking C executable g_tcaf cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_tcaf.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_tcaf.dir/g_tcaf.c.o -o g_tcaf -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Linking C executable g_traj cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_traj.dir/link.txt --verbose=1 [ 98%] Built target g_spol make -f src/tools/CMakeFiles/g_tune_pme.dir/build.make src/tools/CMakeFiles/g_tune_pme.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_tune_pme.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_traj.dir/g_traj.c.o -o g_traj -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_tune_pme.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_tune_pme.dir/depend.internal". Scanning dependencies of target g_tune_pme make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_tune_pme.dir/build.make src/tools/CMakeFiles/g_tune_pme.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Linking C executable g_sigeps cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sigeps.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_tune_pme.dir/g_tune_pme.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_tune_pme.dir/g_tune_pme.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_tune_pme.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sigeps.dir/g_sigeps.c.o -o g_sigeps -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_tune_pme cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_tune_pme.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_tune_pme.dir/g_tune_pme.c.o -o g_tune_pme -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_tcaf make -f src/tools/CMakeFiles/g_vanhove.dir/build.make src/tools/CMakeFiles/g_vanhove.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_vanhove.dir/DependInfo.cmake --color= [ 98%] Built target g_traj make -f src/tools/CMakeFiles/g_velacc.dir/build.make src/tools/CMakeFiles/g_velacc.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_velacc.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_vanhove.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_vanhove.dir/depend.internal". Scanning dependencies of target g_vanhove make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_vanhove.dir/build.make src/tools/CMakeFiles/g_vanhove.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_velacc.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_velacc.dir/depend.internal". Scanning dependencies of target g_velacc make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_velacc.dir/build.make src/tools/CMakeFiles/g_velacc.dir/build [ 98%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/g_vanhove.dir/g_vanhove.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_vanhove.dir/g_vanhove.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_vanhove.c [ 98%] Built target g_sigeps make -f src/tools/CMakeFiles/g_wham.dir/build.make src/tools/CMakeFiles/g_wham.dir/depend [ 98%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_wham.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_velacc.dir/g_velacc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_velacc.dir/g_velacc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_velacc.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_wham.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_wham.dir/depend.internal". Scanning dependencies of target g_wham make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_wham.dir/build.make src/tools/CMakeFiles/g_wham.dir/build Linking C executable g_vanhove cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_vanhove.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_tune_pme /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_vanhove.dir/g_vanhove.c.o -o g_vanhove -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make -f src/tools/CMakeFiles/g_wheel.dir/build.make src/tools/CMakeFiles/g_wheel.dir/depend [ 98%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_wheel.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_wham.dir/g_wham.c.o Linking C executable g_velacc cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_wham.dir/g_wham.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_wham.c cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_velacc.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_wheel.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_wheel.dir/depend.internal". Scanning dependencies of target g_wheel make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_wheel.dir/build.make src/tools/CMakeFiles/g_wheel.dir/build /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_velacc.dir/g_velacc.c.o -o g_velacc -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 85 [ 99%] Linking C executable g_wham cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_wham.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_wheel.dir/g_wheel.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_wheel.dir/g_wheel.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_wheel.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_wham.dir/g_wham.c.o -o g_wham -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Linking C executable g_wheel cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_wheel.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_wheel.dir/g_wheel.c.o -o g_wheel -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread [ 99%] Built target g_vanhove make -f src/tools/CMakeFiles/genbox.dir/build.make src/tools/CMakeFiles/genbox.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genbox.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genbox.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genbox.dir/depend.internal". [ 99%] Built target g_velacc Scanning dependencies of target genbox make -f src/tools/CMakeFiles/genconf.dir/build.make src/tools/CMakeFiles/genconf.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/genbox.dir/build.make src/tools/CMakeFiles/genbox.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genconf.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genconf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genconf.dir/depend.internal". Scanning dependencies of target genconf Building C object src/tools/CMakeFiles/genbox.dir/genbox.c.o make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/genconf.dir/build.make src/tools/CMakeFiles/genconf.dir/build cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/genbox.dir/genbox.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/genbox.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] [ 99%] Built target g_wham make -f src/tools/CMakeFiles/genion.dir/build.make src/tools/CMakeFiles/genion.dir/depend Building C object src/tools/CMakeFiles/genconf.dir/genconf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/genconf.dir/genconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/genconf.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single 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src/tools/CMakeFiles/genion.dir/build.make src/tools/CMakeFiles/genion.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Linking C executable genconf [ 99%] cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/genconf.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/genion.dir/genion.c.o /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/genconf.dir/genconf.c.o -o genconf -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/genion.dir/genion.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/genion.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 85 [ 99%] Built target g_wheel make -f src/tools/CMakeFiles/genrestr.dir/build.make src/tools/CMakeFiles/genrestr.dir/depend Linking C executable genion cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/genion.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genrestr.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/genion.dir/genion.c.o -o genion -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genrestr.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genrestr.dir/depend.internal". Scanning dependencies of target genrestr make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/genrestr.dir/build.make src/tools/CMakeFiles/genrestr.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Building C object src/tools/CMakeFiles/genrestr.dir/genrestr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/genrestr.dir/genrestr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/genrestr.c [ 99%] Built target genbox make -f src/tools/CMakeFiles/make_edi.dir/build.make src/tools/CMakeFiles/make_edi.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/make_edi.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/make_edi.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/make_edi.dir/depend.internal". Built target genconf make -f src/tools/CMakeFiles/make_ndx.dir/build.make src/tools/CMakeFiles/make_ndx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/make_ndx.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/make_ndx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/make_ndx.dir/depend.internal". Linking C executable genrestr cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/genrestr.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/genrestr.dir/genrestr.c.o -o genrestr -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread Scanning dependencies of target make_edi [ 99%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/make_edi.dir/build.make src/tools/CMakeFiles/make_edi.dir/build Built target genion make -f src/tools/CMakeFiles/mk_angndx.dir/build.make src/tools/CMakeFiles/mk_angndx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/mk_angndx.dir/DependInfo.cmake --color= Scanning dependencies of target make_ndx make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/make_ndx.dir/build.make src/tools/CMakeFiles/make_ndx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/mk_angndx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/mk_angndx.dir/depend.internal". [ 99%] Building C object src/tools/CMakeFiles/make_edi.dir/make_edi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/make_edi.dir/make_edi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/make_edi.c Building C object src/tools/CMakeFiles/make_ndx.dir/make_ndx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/make_ndx.dir/make_ndx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/make_ndx.c Scanning dependencies of target mk_angndx make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/mk_angndx.dir/build.make src/tools/CMakeFiles/mk_angndx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Building C object src/tools/CMakeFiles/mk_angndx.dir/mk_angndx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mk_angndx.dir/mk_angndx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/mk_angndx.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Built target genrestr make -f src/tools/CMakeFiles/trjcat.dir/build.make src/tools/CMakeFiles/trjcat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/trjcat.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/trjcat.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/trjcat.dir/depend.internal". Scanning dependencies of target trjcat make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/trjcat.dir/build.make src/tools/CMakeFiles/trjcat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Building C object src/tools/CMakeFiles/trjcat.dir/trjcat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/trjcat.dir/trjcat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/trjcat.c Linking C executable trjcat cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/trjcat.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/trjcat.dir/trjcat.c.o -o trjcat -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Built target trjcat make -f src/tools/CMakeFiles/trjconv.dir/build.make src/tools/CMakeFiles/trjconv.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 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Scanning dependencies of target trjconv make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/trjconv.dir/build.make src/tools/CMakeFiles/trjconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Building C object src/tools/CMakeFiles/trjconv.dir/trjconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/trjconv.dir/trjconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/trjconv.c Linking C executable trjconv cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/trjconv.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/trjconv.dir/trjconv.c.o -o trjconv -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Linking C executable mk_angndx cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/mk_angndx.dir/link.txt --verbose=1 [ 99%] Built target trjconv make -f src/tools/CMakeFiles/trjorder.dir/build.make src/tools/CMakeFiles/trjorder.dir/depend /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/mk_angndx.dir/mk_angndx.c.o -o mk_angndx -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/trjorder.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/trjorder.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/trjorder.dir/depend.internal". Scanning dependencies of target trjorder make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/trjorder.dir/build.make src/tools/CMakeFiles/trjorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Building C object src/tools/CMakeFiles/trjorder.dir/trjorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/trjorder.dir/trjorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/trjorder.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles Linking C executable trjorder cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/trjorder.dir/link.txt --verbose=1 [ 99%] Built target mk_angndx make -f src/tools/CMakeFiles/xpm2ps.dir/build.make src/tools/CMakeFiles/xpm2ps.dir/depend /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/trjorder.dir/trjorder.c.o -o trjorder -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/xpm2ps.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/xpm2ps.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/xpm2ps.dir/depend.internal". Scanning dependencies of target xpm2ps make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/xpm2ps.dir/build.make src/tools/CMakeFiles/xpm2ps.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 100 [100%] Building C object src/tools/CMakeFiles/xpm2ps.dir/xpm2ps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/xpm2ps.dir/xpm2ps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/xpm2ps.c Linking C executable xpm2ps cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/xpm2ps.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/xpm2ps.dir/xpm2ps.c.o -o xpm2ps -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [100%] Built target trjorder Linking C executable make_edi cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/make_edi.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/make_edi.dir/make_edi.c.o -o make_edi -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 100 [100%] Built target xpm2ps make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [100%] Built target make_edi Linking C executable make_ndx cd /builddir/build/BUILD/gromacs-4.5.5/single/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/make_ndx.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/make_ndx.dir/make_ndx.c.o -o make_ndx -rdynamic libgmxana.so.6 ../mdlib/libmd.so.6 -lfftw3f -lxml2 ../gmxlib/libgmx.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [100%] Built target make_ndx make[1]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 0 + cd .. + mkdir double + cd double + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export FFLAGS + /usr/bin/cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DCMAKE_SKIP_RPATH:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=ON -D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=lib64 -D GMX_DOUBLE=ON .. -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. 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found -- Looking for vprintf -- Looking for vprintf - found -- Looking for memcmp -- Looking for memcmp - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Looking for _aligned_malloc -- Looking for _aligned_malloc - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for isnan -- Looking for isnan - found -- Looking for _isnan -- Looking for _isnan - not found -- Looking for isfinite -- Looking for isfinite - not found -- Looking for _isfinite -- Looking for _isfinite - not found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for cbrt in m -- Looking for cbrt in m - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of bool -- Check size of bool - failed -- Check size of int -- Check size of int - done -- Check size of long int -- Check size of long int - done -- Check size of long long int -- Check size of long long int - done -- Check size of off_t -- Check size of off_t - done -- Check size of void * -- Check size of void * - done -- Check size of uid_t -- Check size of uid_t - done -- Check size of gid_t -- Check size of gid_t - done -- Check size of size_t -- Check size of size_t - done -- Check size of off_t -- Check size of off_t - done -- Check if the system is big endian -- Searching 16 bit integer -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - big endian -- checking for module 'libxml-2.0' -- found libxml-2.0, version 2.7.6 -- Found LibXml2: /usr/lib64/libxml2.so -- Looking for include files CMAKE_HAVE_PTHREAD_H -- Looking for include files CMAKE_HAVE_PTHREAD_H - found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Looking for include files HAVE_SCHED_H -- Looking for include files HAVE_SCHED_H - found -- Looking for sysconf -- Looking for sysconf - found -- Atomics found -- Setting build user & time -- Setting build user & time - OK -- Checking floating point format -- Checking floating point format - unknown -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for return type of signals -- Checking for return type of signals - void -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for inline keyword -- Checking for inline keyword - inline -- Checking for inline keyword -- Checking for inline keyword - inline -- Checking for pipe support -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - 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Scanning dependencies of target gmx make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 0%] [ 0%] [ 0%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/princ.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/princ.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c Building C object src/gmxlib/CMakeFiles/gmx.dir/topsort.c.o [ 0%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/topsort.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_fatal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_fatal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_fatal.c Building C object src/gmxlib/CMakeFiles/gmx.dir/random.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/random.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c: In function 'gmx_sort_ilist_fe': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c:185: warning: unused variable 'bPert' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_fatal.c:150: warning: 'bputi' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c: In function 'maxwell_speed': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c:93: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c:92: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c:48: warning: 'm_op' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c:249: warning: 'dump_shit' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/checkpoint.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/checkpoint.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/dihres.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/dihres.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 0%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_real': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:448: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_ints': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:459: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_doubles': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:526: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_rvecs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:591: warning: unused variable 'n3' Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_cyclecounter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_cyclecounter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_cyclecounter.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpt_header': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:700: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpt_files': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1043: warning: unused variable 'j' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 1 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'write_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1159: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1154: warning: unused variable 'flag_64bit' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'read_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1459: warning: unused variable 'filename' [ 1%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'list_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2001: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2001: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2000: warning: unused variable 'indent' Building C object src/gmxlib/CMakeFiles/gmx.dir/warninp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/warninp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/warninp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:429: warning: 'do_cpte_reals' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c: In function 'ta_dihres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c:78: warning: unused variable 'dp2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c:77: warning: unused variable 'typep' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sfactor.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sfactor.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sfactor.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used [ 1%] /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/ifunc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ifunc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ifunc.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ffscanf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ffscanf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ffscanf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_system_xdr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_system_xdr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_system_xdr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/macros.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/macros.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/macros.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/shift_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/shift_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 2 [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/atomprop.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/atomprop.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c: In function 'shift_LRcorrection': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:271: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:267: warning: unused variable 'qtot' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:266: warning: unused variable 'isp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:384: warning: 'rgbset' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c: In function 'gmx_atomprop_init': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c:246: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrnb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrnb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrnb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 2%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/tpxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/tpxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_pullgrp': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:212: warning: unused variable 'i' [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/calch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/calch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_iparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:931: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ilist': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1179: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1200: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ilists': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1262: warning: unused variable 'bDum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1261: warning: unused variable 'renum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1261: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_grps': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1382: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1498: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1498: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_atomtypes': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1525: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_moltype': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1678: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_molblock': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1706: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_mtop': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1834: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2046: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'read_tpx_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2347: warning: unused variable 'ltop' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'read_tps_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2376: warning: unused variable 'topconv' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c: In function 'gen_waterhydrogen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c:82: warning: unused variable 'kkk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/wman.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/wman.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'mydate': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:202: warning: unused variable 'num' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'print_tty_formatted': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:551: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_wikiman': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:672: warning: unused variable 'tmp2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:671: warning: unused variable 'link' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_htmlman': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:723: warning: unused variable 'link' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_py': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:966: warning: unused variable 'bHidden' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/string2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/string2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c: In function 'ltrim': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c:137: warning: unused variable 'tr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/matio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/matio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pargs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pargs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c: In function 'write_xpm_map_split': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'fac' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:661: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c: In function 'print_pargs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'buf2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 3 [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_asc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_asc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_asc.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/index.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/index.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'analyse_prot': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:365: warning: unused variable 'nnpres' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'gmx_residuetype_add': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:514: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'gmx_residuetype_init': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:546: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:545: warning: unused variable 'p' [ 3%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'analyse': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:734: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:732: warning: unused variable 'j' Building C object src/gmxlib/CMakeFiles/gmx.dir/xtcio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xtcio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xtcio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pdbio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pdbio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: In function 'gmx_conect_add': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:681: warning: unused variable 'i' [ 3%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: In function 'read_pdbfile': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:705: warning: unused variable 'chidmax' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:704: warning: unused variable 'nres_ter_prev' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/readinp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/readinp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: In function 'get_einp': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c:283: warning: unused variable 'warn_buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: In function 'get_eenum': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c:456: warning: unused variable 'dum' [ 3%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not usedBuilding C object src/gmxlib/CMakeFiles/gmx.dir/main.c.o /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not usedcd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/main.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'par_fn': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:140: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'gmx_log_open': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:259: warning: unused variable 'testlen' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'init_multisystem': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:485: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'init_par': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:522: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:377: warning: 'comm_args' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/orires.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/orires.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 4 [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/calcgrid.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/calcgrid.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c: In function 'init_orires': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c:58: warning: unused variable 'nr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c: In function 'calc_grid': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c:98: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 4%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/sortwater.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sortwater.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sortwater.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 4%] [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c Building C object src/gmxlib/CMakeFiles/gmx.dir/pbc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pbc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'set_default_time_unit': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:255: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'set_default_xvg_format': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:287: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:286: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'parse_common_args': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:578: warning: unused variable 'envstr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:577: warning: unused variable 'newdesc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:577: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:536: warning: unused variable 'npri_pa' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:529: warning: unused variable 'mantp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'low_set_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:285: warning: unused variable 'bXY' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'put_atom_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1195: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'put_atoms_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1209: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1209: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:409: warning: 'pdesc' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trnio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trnio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trnio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_remove': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:339: warning: unused variable 'prev' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_open': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:438: warning: unused variable 'xdrid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:435: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_fopen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:640: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_fclose': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:654: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_int_get_file_position': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:783: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_get_output_file_positions': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:858: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:837: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:835: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:834: warning: unused variable 'pos_lo' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:834: warning: unused variable 'pos_hi' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:833: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:833: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_int_fsync': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:1005: warning: unused variable 'filen' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/maths.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/maths.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mtxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c: In function 'gmx_erfc': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 'z4' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 'z2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 's3' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 's2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 's1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 'r2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 'r1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: In function 'gmx_mtxio_write': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c:92: warning: unused variable 'bRead' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: In function 'gmx_mtxio_read': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c:166: warning: unused variable 'bRead' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 5 [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xvgr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xvgr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 5%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/libxdrf.c.o [ 5%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/libxdrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c Building C object src/gmxlib/CMakeFiles/gmx.dir/replace.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/replace.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/replace.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'xvgropen_type': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:287: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'fgets3': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:442: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'read_xvg_legend': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:546: warning: unused variable 'ptr1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:546: warning: unused variable 'ptr0' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'read_xvg_time': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:697: warning: unused variable 'tend' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr3dfcoord': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:820: warning: unused variable 'xdrid' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xtc_get_next_frame_start': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1546: warning: unused variable 'inp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr_xtc_seek_time': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1693: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr_xtc_get_last_frame_number': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1882: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/viewit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/viewit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/viewit.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/strdb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/strdb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/strdb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/enxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/enxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'do_enxnms': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:392: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'do_eheader': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:448: warning: unused variable 'tempfix_nr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:446: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'open_enx': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:723: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'get_enx_state': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:1071: warning: unused variable 'pcouplmu_nm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:375: warning: 'gen_units' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 5%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 6 Building C object src/gmxlib/CMakeFiles/gmx.dir/splitter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/splitter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/filenm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/filenm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: In function 'set_default_file_name': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c:216: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: In function 'add_suffix_to_output_names': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c:951: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_force2': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:116: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'mk_border': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:346: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_blocks': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:424: warning: unused variable 'bSHK' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:420: warning: unused variable 'last_shk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:419: warning: unused variable 'ai' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:419: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'merge_sid': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:662: warning: unused variable 'nChanged' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'gen_sblocks': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:760: warning: unused variable 'isid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'istart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'find_constraint_range_recursive': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:866: warning: unused variable 'nconstr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'pd_determine_constraints_range': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:890: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:890: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'minidx' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'ihome' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'minhome' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:932: warning: unused variable 'ia' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nrd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nra' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nvsite_constr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'ftype' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'nodeid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'bstart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'send' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'sstart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'maxatom' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'atom' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'mj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:832: warning: 'block2blocka' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rmpbc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rmpbc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rmpbc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/inputrec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/inputrec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/inputrec.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rando.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rando.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rando.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/bondfree.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/vmddlopen.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmddlopen.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'FENE_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:242: warning: unused variable 'dr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'do_1_thole': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:652: warning: unused variable 'r12n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'posres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1254: warning: unused variable 'ki' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'cmap_dihs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1642: warning: unused variable 'psi2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1641: warning: unused variable 'psi1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1637: warning: unused variable 'l4' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'bonded_tab': [ 6%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2350: warning: unused variable 'f' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2350: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'tab_angles': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2475: warning: unused variable 'snt' Building C object src/gmxlib/CMakeFiles/gmx.dir/txtdump.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: At top level:cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/txtdump.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c: In function 'choose_ff': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c:441: warning: unused variable 'eFF' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_qm_opts': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:991: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_block_title': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1037: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_blocka_title': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1050: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_block': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1103: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_atom': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1225: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1260: warning: unused variable 'grpnr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_header': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1423: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1063: warning: 'low_pr_block' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 7 [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/writeps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/writeps.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxcpp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxcpp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: In function 'cpp_open_file': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c:188: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: In function 'cpp_close_file': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c:577: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_xdr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_xdr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_xdr.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 7%] [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_matrix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_matrix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c Building C object src/gmxlib/CMakeFiles/gmx.dir/sighandler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sighandler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sighandler.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_arpack.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_arpack.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_arpack.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: In function 'free_matrix': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c:63: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: In function 'multi_regression': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c:174: warning: unused variable 'niter' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/vmdio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c: In function 'load_vmd_library': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c:234: warning: unused variable 'filename' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 8 [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/names.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/names.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/names.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrjac.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrjac.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrjac.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/confio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/confio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/do_fit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/do_fit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: In function 'read_espresso_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:451: warning: unused variable 'npar' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:451: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: In function 'read_stx_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:1397: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:1392: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: In function 'calc_fit_R': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c:104: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: In function 'do_fit_ndim': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c:215: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:880: warning: 'get_conf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/typedefs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/typedefs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_block': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:108: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_blocka': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:118: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_atom': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:131: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:183: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_state': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:533: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/symtab.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/symtab.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/symtab.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mvdata.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mvdata.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_atoms': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:169: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:187: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:327: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:349: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_inputrec': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:466: warning: unused variable 'bAlloc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_molblock': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:497: warning: unused variable 'bAlloc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:312: warning: 'bc_idef' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 9 [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sparsematrix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sparsematrix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sparsematrix.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gbutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gbutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gbutil.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mshift.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mshift.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: In function 'compact_graph': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c:249: warning: unused variable 'e' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: In function 'done_graph': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c:405: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 9%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/md5.c.o [ 9%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/md5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/md5.c Building C object src/gmxlib/CMakeFiles/gmx.dir/futil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/futil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c: In function 'ffopen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c:446: warning: unused variable 'bf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/tcontrol.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/tcontrol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tcontrol.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used[ 9%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/ewald_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ewald_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ewald_util.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/smalloc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/smalloc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c: In function 'save_free_aligned': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c:356: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c:356: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 10 [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/oenv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/oenv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/oenv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/3dview.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_sort.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_sort.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_sort.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c: In function 'reset_view': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c:281: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mtop_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_atomnr_to_molblock_ind': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:150: warning: unused variable 'atoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_atominfo_global': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:177: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_ilistloop_all_next': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:449: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_global_cgs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:503: warning: unused variable 'atoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gen_local_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:773: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:773: warning: unused variable 'ftype_dest' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used [ 10%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nrama.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrama.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/wgms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/wgms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wgms.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: In function 'get_dih2': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:182: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: In function 'init_rama': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:312: warning: unused variable 'ePBC' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used[ 10%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/rbin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rbin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rbin.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:179: warning: 'get_dih2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 11 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 11%] [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/chargegroup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/chargegroup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/chargegroup.c Building C object src/gmxlib/CMakeFiles/gmx.dir/network.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/network.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/invblock.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/invblock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/invblock.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: In function 'gmx_setup': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:82: warning: unused variable 'flag' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:82: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:80: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: In function 'gmx_setup_nodecomm': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:262: warning: unused variable 'num' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:262: warning: unused variable 'mpi_hostname' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'ni' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'ng' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'hostnum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'resultlen' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'rank' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:260: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xdrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xdrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xdrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/disre.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/disre.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_rw.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_rw.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_rw.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: In function 'calc_disres_R_6': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'jt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'kj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'ki' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: In function 'ta_disres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:372: warning: unused variable 'jt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:372: warning: unused variable 'it' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 11%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_bin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_bin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_bin.c [ 11%] Building C object src/gmxlib/CMakeFiles/gmx.dir/cinvsqrtdata.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/cinvsqrtdata.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/cinvsqrtdata.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 12 /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/copyrite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/copyrite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_random.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_random.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: In function 'cool_quote': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c:193: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: In function 'please_cite': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c:535: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c: In function 'gmx_rng_update': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c:217: warning: unused variable 'lastx' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 12%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selvalue.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selvalue.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selvalue.c [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_permute.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: In function 'init_output_permute': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c:192: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: In function 'evaluate_permute': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c:240: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_same.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selhelp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selhelp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selhelp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 12%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c: In function 'evaluate_same_str': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c:499: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 13 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selelem.c.o /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selelem.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selelem.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/scanner.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/scanner.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/scanner.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used scanner.c:1396: warning: 'yyunput' defined but not used scanner.c:1438: warning: 'input' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/parsetree.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/parsetree.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_insolidangle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_insolidangle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_selelem_set_method': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:556: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_sel_init_comparison': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:652: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_sel_init_modifier': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:835: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/scanner_internal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/scanner_internal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/scanner_internal.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: In function 'evaluate_insolidangle': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:476: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: In function 'store_surface_point': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:829: warning: unused variable 'bin' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:829: warning: unused variable 'pbin' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:213: warning: 'set_comg_insolidangle' declared 'static' but never defined /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/symrec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c: In function 'add_symbol': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c:395: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used [ 13%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/parser.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/parser.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parser.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 13%] [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/compiler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/compiler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_distance.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_distance.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_distance.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 14 [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/mempool.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/mempool.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/mempool.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c: In function 'analyze_static': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c:2004: warning: unused variable 'next' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c:2004: warning: unused variable 'child' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/params.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/params.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_compare.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_compare.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_compare.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c: In function 'parse_values_varnum_expr': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c:676: warning: unused variable 'expr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 14%] [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_keywords.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_keywords.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_keywords.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_position.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_position.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selection.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selection.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selection.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 14%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_simple.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_simple.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 15 [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selmethod.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selmethod.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selmethod.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/evaluate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/evaluate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/evaluate.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_merge.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_merge.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c: In function 'init_merge': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c:182: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/trajana.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/position.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/position.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: In function 'gmx_ana_traj_free': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c:322: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: In function 'gmx_ana_init_selections': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c:1200: warning: unused variable 'bOk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/poscalc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/nbsearch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/nbsearch.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: In function 'merge_to_base': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c:797: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: In function 'gmx_ana_poscalc_update': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c:1282: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/displacement.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/displacement.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 16 [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/indexutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/indexutil.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 16%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/centerofmass.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c: In function 'gmx_calc_cog': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c:55: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: In function 'gmx_stats_dump_xy': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c:449: warning: unused variable 'ok' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: In function 'gmx_stats_make_histogram': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c:505: warning: unused variable 'ok' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used [ 16%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statistics/histogram.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/histogram.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_generic_cg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_generic_cg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c: In function 'gmx_nb_generic_cg_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:83: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:62: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:61: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nonbonded.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nonbonded.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: In function 'do_nonbonded': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:313: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:311: warning: unused variable 'bWater' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:309: warning: unused variable 'sz' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: In function 'do_listed_vdw_q': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:664: warning: unused variable 'tmplist' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:655: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 17 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 16%] [ 17%] [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_generic.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_free_energy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_free_energy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_generic.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel230.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel230.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c: In function 'gmx_nb_free_energy_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:102: warning: unused variable 'H' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:102: warning: unused variable 'G' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:91: warning: unused variable 'rinvsix' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:88: warning: unused variable 'vcoul' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c: In function 'gmx_nb_generic_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:81: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:61: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:60: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: In function 'nb_kernel230': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: In function 'nb_kernel230nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c:336: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 17%] [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel213.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel213.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel312.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel312.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel101.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel101.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: In function 'nb_kernel312': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: In function 'nb_kernel312nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c:733: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: In function 'nb_kernel213': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used [ 17%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: In function 'nb_kernel213nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c:424: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel223.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel223.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: In function 'nb_kernel101': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: In function 'nb_kernel101nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c:368: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: In function 'nb_kernel223': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: In function 'nb_kernel223nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c:427: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel334.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel334.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 18 [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel210.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel210.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: In function 'nb_kernel334': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: In function 'nb_kernel334nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c:798: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 18%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: In function 'nb_kernel210': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: In function 'nb_kernel210nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c:304: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel112.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel112.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: In function 'nb_kernel112': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: In function 'nb_kernel112nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c:574: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In function 'nb_kernel200': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In function 'nb_kernel200nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:286: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 18%] [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel130.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel130.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel211.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel211.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: In function 'nb_kernel130': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: In function 'nb_kernel211': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: In function 'nb_kernel211nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c:390: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: In function 'nb_kernel130nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c:334: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel214.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel214.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: In function 'nb_kernel214': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: In function 'nb_kernel214nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c:622: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 18%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel110.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel110.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 19 [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel131.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel131.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c: In function 'setup_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c:113: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: In function 'nb_kernel110': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: In function 'nb_kernel110nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c:302: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: In function 'nb_kernel131': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: In function 'nb_kernel131nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c:418: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel232.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel232.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel303.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel303.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: In function 'nb_kernel232': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: In function 'nb_kernel232nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c:616: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel304.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel304.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: In function 'nb_kernel303': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: In function 'nb_kernel303nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel124.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel124.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: In function 'nb_kernel304': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: In function 'nb_kernel304nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c:715: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: In function 'nb_kernel124': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: In function 'nb_kernel124nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c:615: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel430.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel430.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c: In function 'nb_kernel430': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c:105: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel221.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel221.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: In function 'nb_kernel221': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: In function 'nb_kernel221nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c:392: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 20 [ 20%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel420.c.o [ 20%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel420.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel400.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel400.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c: In function 'nb_kernel420': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c:105: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c: In function 'nb_kernel400': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c:100: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used/builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 20%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel100.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel100.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 20%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: In function 'nb_kernel100': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: In function 'nb_kernel100nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c:284: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel030.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel030.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel132.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel132.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel302.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel302.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: In function 'nb_kernel030': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: In function 'nb_kernel030nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c:322: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel233.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel233.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: In function 'nb_kernel132': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: In function 'nb_kernel132nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c:606: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: In function 'nb_kernel302': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: In function 'nb_kernel302nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c:715: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: In function 'nb_kernel233': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: In function 'nb_kernel233nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c:456: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel320.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel320.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: In function 'nb_kernel320': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: In function 'nb_kernel320nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c:327: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 21 [ 21%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel123.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel123.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel204.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel204.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: In function 'nb_kernel123': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: In function 'nb_kernel123nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: In function 'nb_kernel204': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: In function 'nb_kernel204nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c:568: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c: In function 'setup_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c:114: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel313.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel313.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel314.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel314.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: In function 'nb_kernel313': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: In function 'nb_kernel313nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c:476: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 21%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: In function 'nb_kernel314': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: In function 'nb_kernel314nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c:770: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel333.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel333.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel311.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: In function 'nb_kernel333': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c:84: warning: unused variable 'gbtabscale'cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel311.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: In function 'nb_kernel333nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c:504: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: In function 'nb_kernel311': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: In function 'nb_kernel311nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c:443: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 22 [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel331.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel331.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: In function 'nb_kernel331': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: In function 'nb_kernel331nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c:460: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel113.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel113.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: In function 'nb_kernel113': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: In function 'nb_kernel113nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c:420: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 22%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel121.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel121.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel010.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel010.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: In function 'nb_kernel121': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: In function 'nb_kernel121nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c:388: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: In function 'nb_kernel010': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c:85: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: In function 'nb_kernel010nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c:292: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel201.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel201.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel330.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel330.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel102.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel102.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: In function 'nb_kernel201': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: In function 'nb_kernel201nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c:372: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: In function 'nb_kernel330': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: In function 'nb_kernel330nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c:342: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 22%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: In function 'nb_kernel102': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c:84: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel020.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel020.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: In function 'nb_kernel102nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c:558: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: In function 'nb_kernel020': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: In function 'nb_kernel020nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c:294: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 23 [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel231.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel231.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel203.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel203.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 23%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: In function 'nb_kernel231': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: In function 'nb_kernel231nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c:422: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel133.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel133.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: In function 'nb_kernel203': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: In function 'nb_kernel203nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c:372: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: In function 'nb_kernel133': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: In function 'nb_kernel133nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c:452: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel224.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel224.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: In function 'nb_kernel224': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: In function 'nb_kernel224nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c:625: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used [ 23%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel323.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel323.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel103.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel103.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: In function 'nb_kernel323': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: In function 'nb_kernel323nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c:479: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: In function 'nb_kernel103': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: In function 'nb_kernel103nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c:368: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel322.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel322.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: In function 'nb_kernel322': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: In function 'nb_kernel322nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c:735: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 24 [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel104.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel104.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel324.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel324.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: In function 'nb_kernel104': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: In function 'nb_kernel104nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c:558: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel410.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel410.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: In function 'nb_kernel324': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: In function 'nb_kernel324nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c:773: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c: In function 'nb_kernel410': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c:106: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel202.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel202.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel212.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel212.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: In function 'nb_kernel202': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: In function 'nb_kernel202nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c:568: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel114.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel114.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: In function 'nb_kernel212': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: In function 'nb_kernel212nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c:584: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: In function 'nb_kernel114': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: In function 'nb_kernel114nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c:612: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel222.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel222.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 25 [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel332.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel332.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: In function 'nb_kernel222': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: In function 'nb_kernel222nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c:586: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: In function 'nb_kernel332': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: In function 'nb_kernel332nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c:750: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel300.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel300.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: In function 'nb_kernel300': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: In function 'nb_kernel300nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c:305: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 25%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_c.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_c.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 25%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel301.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel301.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel134.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel134.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: In function 'nb_kernel301': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: In function 'nb_kernel301nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: In function 'nb_kernel134': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: In function 'nb_kernel134nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c:644: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used [ 25%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel321.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel321.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: In function 'nb_kernel321': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: In function 'nb_kernel321nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c:445: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 25%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel234.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel234.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c [ 25%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel310.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel310.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 26 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: In function 'nb_kernel234': [ 26%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: In function 'nb_kernel234nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c:654: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel122.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel122.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: In function 'nb_kernel310': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: In function 'nb_kernel310nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c:325: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: In function 'nb_kernel122': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: In function 'nb_kernel122nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c:576: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel111.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel111.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: In function 'nb_kernel111': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: In function 'nb_kernel111nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c:386: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 26%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel120.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel120.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: In function 'nb_kernel120': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: In function 'nb_kernel120nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c:304: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel220.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel220.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sger.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sger.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sger.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/srot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/srot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/srot.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dswap.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: In function 'nb_kernel220': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c:84: warning: unused variable 'gbtabscale' cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dswap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dswap.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: In function 'nb_kernel220nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c:306: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 27 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 27%] [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sgemm.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dasum.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dasum.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dasum.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sgemm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sgemm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/daxpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/daxpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/daxpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/idamax.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/idamax.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/idamax.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 27%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dger.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dger.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dger.c [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dscal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dscal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dscal.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 27%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 28 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrsm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrsm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrsm.c [ 28%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ddot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ddot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ddot.c [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ssyr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ssyr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssyr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sscal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sscal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sscal.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 28%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsyr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsyr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsyr2.c [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/isamax.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/isamax.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/isamax.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 28%] [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dgemv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dgemv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dgemv.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsyr2k.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsyr2k.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsyr2k.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 29 [ 29%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dgemm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dgemm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dgemm.c [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrmv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrmv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrmv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dcopy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dcopy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dcopy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 29%] [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sasum.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sgemv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sgemv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sgemv.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sasum.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sasum.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 29%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsymv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsymv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsymv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 29%] Building C object 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-fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/saxpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/saxpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 30%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sswap.c.o [ 30%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib 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-fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormqr.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstein.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstein.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstein.c /usr/bin/cmake -E cmake_progress_report 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src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarnv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarnv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarnv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasv2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasv2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasv2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasr.c.o -c 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object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slagts.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slagts.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slagts.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarft.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 33%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarft.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 33%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 33%] [ 33%] [ 33%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaruv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaruv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaruv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrbx.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgeqrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgeqrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgeqrf.c [ 33%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrbx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrbx.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormlq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormlq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormlq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 34 [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorg2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorg2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorg2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasrt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasrt.c.o -c 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-I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd8.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd8.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 34%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slange.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o 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src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd3.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetri.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetri.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 35%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq1.c.o 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-I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorm2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorm2r.c [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorglq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorglq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorglq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 35%] Building C object 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-Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd0.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd0.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd7.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd7.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd7.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 36%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq6.c [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorglq.c.o cd 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-I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 37%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlacpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlacpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlacpy.c 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormql.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormql.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetf2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetf2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetf2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 38%] Building C object 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-Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasda.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasda.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgebrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgebrd.c.o -c 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object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstebz.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaswp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstebz.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaswp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaswp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarfg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarfg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarfg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaev2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaev2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaev2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 44 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 44%] [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slascl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slascl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slascl.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slapy2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slapy2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slapy2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dtrti2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dtrti2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dtrti2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 44%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slassq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slassq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slassq.c [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 44%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 45 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq4.c [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetf2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetf2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetf2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 45%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrex.c.o [ 45%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrex.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd7.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd7.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd7.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaed6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaed6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaed6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssytrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssytrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssytrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgelq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgelq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgelq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorm2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorm2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorm2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 45%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 46 [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd5.c.o cd 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlansy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlansy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlansy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasdq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasdq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasdq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlanst.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlanst.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlanst.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsytd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsytd2.c.o -c 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlartg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlartg.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dbdsqr.c.o [ 49%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dbdsqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd2.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c: In function 'dbdsqr_': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c:61: warning: unused variable 'ftmp' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 49%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgebd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgebd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgebd2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaebz.c.o -c 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-I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlange.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlange.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgelq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgelq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgelq2.c 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-I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssyevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssyevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasrt2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 51 [ 51%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlar1vx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlar1vx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlar1vx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 51%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slagtf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slagtf.c.o -c 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-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorg2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorg2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetrs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include 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cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd4.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dbdsdc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dbdsdc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsdc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq5.c.o -c 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src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorm2l.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorm2l.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorm2l.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarfg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgebrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlagts.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlagts.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlagts.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 55 [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormtr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq6.c [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slanst.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slanst.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slanst.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgeqr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgelqf.c [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/alltoall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/alltoall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/alltoall.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/p2p_protocol.c.o cd 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/builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 56 /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/barrier.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/barrier.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/barrier.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 56%] /usr/bin/cmake -E cmake_progress_report 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-Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/bcast.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/bcast.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/p2p_wait.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/p2p_wait.c.o -c 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but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/collective.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/collective.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/collective.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 56%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/profile.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/profile.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/profile.c [ 56%] /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/comm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/comm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/comm.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/pthreads.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 57 [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/errhandler.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/pthreads.c:165: warning: 'tMPI_Set_affinity' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/reduce.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/reduce.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/reduce.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/event.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/event.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/event.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/reduce_fast.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/reduce_fast.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/reduce_fast.c [ 57%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/gather.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/gather.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/gather.c [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/scatter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/scatter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/scatter.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 58 /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used [ 57%] [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/group.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/group.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/group.c Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_init.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/tmpi_init.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/tmpi_init.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 58%] [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/topology.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/topology.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/topology.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/list.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/list.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/list.c [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/type.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/type.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/type.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/lock.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/lock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/lock.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 58%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/numa_malloc.c.o [ 58%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/thread_mpi/numa_malloc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/thread_mpi/numa_malloc.c Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/once.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/gcc -Dgmx_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 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CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o CMakeFiles/gmx.dir/gmx_lapack/dlagts.c.o CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o CMakeFiles/gmx.dir/gmx_lapack/slanst.c.o CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o CMakeFiles/gmx.dir/thread_mpi/alltoall.c.o CMakeFiles/gmx.dir/thread_mpi/p2p_protocol.c.o CMakeFiles/gmx.dir/thread_mpi/barrier.c.o CMakeFiles/gmx.dir/thread_mpi/p2p_send_recv.c.o CMakeFiles/gmx.dir/thread_mpi/bcast.c.o CMakeFiles/gmx.dir/thread_mpi/p2p_wait.c.o CMakeFiles/gmx.dir/thread_mpi/collective.c.o CMakeFiles/gmx.dir/thread_mpi/profile.c.o CMakeFiles/gmx.dir/thread_mpi/comm.c.o CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o CMakeFiles/gmx.dir/thread_mpi/reduce.c.o CMakeFiles/gmx.dir/thread_mpi/event.c.o CMakeFiles/gmx.dir/thread_mpi/reduce_fast.c.o CMakeFiles/gmx.dir/thread_mpi/gather.c.o CMakeFiles/gmx.dir/thread_mpi/scatter.c.o CMakeFiles/gmx.dir/thread_mpi/group.c.o CMakeFiles/gmx.dir/thread_mpi/tmpi_init.c.o CMakeFiles/gmx.dir/thread_mpi/topology.c.o CMakeFiles/gmx.dir/thread_mpi/list.c.o CMakeFiles/gmx.dir/thread_mpi/type.c.o CMakeFiles/gmx.dir/thread_mpi/lock.c.o CMakeFiles/gmx.dir/thread_mpi/numa_malloc.c.o CMakeFiles/gmx.dir/thread_mpi/once.c.o -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib && /usr/bin/cmake -E cmake_symlink_library libgmx_d.so.6 libgmx_d.so.6 libgmx_d.so make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 [ 58%] Built target gmx make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib/CMakeFiles/md.dir/depend.internal". Scanning dependencies of target md make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 59 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 59%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 59%] [ 59%] Building C object src/mdlib/CMakeFiles/md.dir/mdatom.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdatom.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/mdlib/CMakeFiles/md.dir/sim_util.c.o Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_mkl.c.o [ 59%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_mkl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_mkl.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/sim_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall_sse2_single.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 59%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdebin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c: In function 'init_mdatoms': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:55: warning: unused variable 'ilist' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'nmol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'mb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 59%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'calc_virial': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:362: warning: unused variable 'virtest' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:361: warning: unused variable 'j' Building C object src/mdlib/CMakeFiles/md.dir/coupling.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/coupling.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'finish_run': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1358: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'init_md': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1467: warning: unused variable 'mod' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1467: warning: unused variable 'tmpt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1466: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1466: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'init_mdebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:544: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:136: warning: unused variable 'nh' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'upd_mdebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:650: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'print_ebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:929: warning: unused variable 'enxlambda_data' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:918: warning: unused variable 'nor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:918: warning: unused variable 'ndr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'NHC_trotter': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:62: warning: unused variable 'jmax' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'boxv_trotter': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:184: warning: unused variable 'Winvm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:183: warning: unused variable 'T' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'i' [ 59%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'berendsen_pcoupl': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:446: warning: unused variable 'ptr' Building C object src/mdlib/CMakeFiles/md.dir/qm_orca.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_orca.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'trotter_update': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:660: warning: unused variable 'consk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:657: warning: unused variable 'dumvir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:657: warning: unused variable 'dumpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'nd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'kT' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'reft' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'qmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'bmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'dvdlcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'pcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'ecorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:651: warning: unused variable 'ntgrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:651: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'init_npt_vars': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:784: warning: unused variable 'dumvir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:784: warning: unused variable 'dumpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:783: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'dvdlcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'pcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'ecorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:780: warning: unused variable 'tcstat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:779: warning: unused variable 'gc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:779: warning: unused variable 'ntgrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'NPT_energy': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'Q' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'W' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'dbaro' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:998: warning: unused variable 'tau' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:998: warning: unused variable 'eta' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'ngtcall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'qmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'bmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c: In function 'read_orca_output': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c:261: warning: unused variable 'atnum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 59%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftw3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftw3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw3.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw3.c:44: warning: 'gmx_fft_threads_initialized' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 60 [ 60%] Building C object src/mdlib/CMakeFiles/md.dir/partdec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/partdec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 60%] Building C object src/mdlib/CMakeFiles/md.dir/iteratedconstraints.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/iteratedconstraints.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 60%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftw2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftw2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 60%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_double.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_sse2_double.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_sse2_double.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'gmx_tx': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:101: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:100: warning: unused variable 'flag' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c: In function 'done_iterating': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c:103: warning: unused variable 'xmin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'init_partdec_constraint': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:508: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'init_partdec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:563: warning: unused variable 'nodeid' /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'create_vsitelist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:769: warning: unused variable 'minidx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'setup_parallel_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:831: warning: unused variable 'recvbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:831: warning: unused variable 'sendbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 60%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:765: warning: 'create_vsitelist' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/vsite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/vsite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used [ 60%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/qmmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qmmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 60%] Building C object src/mdlib/CMakeFiles/md.dir/rf_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/rf_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'constr_vsiten': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:376: warning: unused variable 'xs' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'construct_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'rtmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'vtmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'reftmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:417: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite2': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:588: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite3FD': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:703: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite_f': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1188: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'count_intercg_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1344: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'get_vsite_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1383: warning: unused variable 'cg_c' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'init_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1494: warning: unused variable 'cg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c: In function 'RF_excl_correction': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c:58: warning: unused variable 'top' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c: In function 'update_QMMMrec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c:740: warning: unused variable 'MMatoms' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c:140: warning: 'int_comp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 61 [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_box.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_box.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_box.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_parallel_3dfft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c:46: warning: 'copy_int_array' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c:57: warning: 'make_slab2grid' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/pppm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pppm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/shellfc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/shellfc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c: In function 'gmx_pppm_init': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:508: warning: unused variable 'spacing' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:508: warning: unused variable 'box_diag' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:507: warning: unused variable 'tol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:506: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:506: warning: unused variable 'r1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:505: warning: unused variable 'grids' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'porder' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'nz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'nx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/minimize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/minimize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 61%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'predict_shells': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:118: warning: unused variable 'dt_3' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:118: warning: unused variable 'dt_2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'init_shell_flexcon': Building C object src/mdlib/CMakeFiles/md.dir/shakef.c.o /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:200: warning: unused variable 'mt' cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/shakef.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'init_adir': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:689: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:689: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:686: warning: unused variable 'scale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'gt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'ga' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'gf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'relax_shell_flexcon': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:777: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:772: warning: unused variable 'xiS' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:772: warning: unused variable 'xiH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:770: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'get_f_norm_max': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:185: warning: unused variable 'fmax2_0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'cshake': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tiz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tiy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tix' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'vec_shakef': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'rvscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'rscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'vscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'crattle': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:909: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:895: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:894: warning: unused variable 'sfm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tiz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tiy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tix' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'jmdt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'imdt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'diff' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'rijd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:456: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:454: warning: unused variable 'mytol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_lbfgs': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:1431: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_steep': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2059: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2049: warning: unused variable 'dvdlambda' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2048: warning: unused variable 'constepsize' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_nm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2269: warning: unused variable 'fmax' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2269: warning: unused variable 'fnorm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2255: warning: unused variable 'bNS' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:83: warning: 'pv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:569: warning: 'do_x_step' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:591: warning: 'do_x_sub' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/md_support.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/md_support.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c: In function 'compute_globals': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:297: warning: unused variable 'temp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:297: warning: unused variable 'ekin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:294: warning: unused variable 'bVV' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:293: warning: unused variable 'shakeall_vir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 61%] Building C object src/mdlib/CMakeFiles/md.dir/ebin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ebin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c: In function 'add_ebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:127: warning: unused variable 'sigma' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:127: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:54: warning: 'rms_ener' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 62 [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall_sse2_double.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/vcm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/vcm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/fft5d.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/fft5d.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/fft5d.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/constr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/constr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'calc_vcm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'zz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'yz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'yy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'do_stopcm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:170: warning: unused variable 'tm_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:170: warning: unused variable 'tm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:169: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'check_cm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:249: warning: unused variable 'Tcm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/fft5d.c:115: warning: 'lpfactor' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'too_many_constraint_warnings': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:185: warning: unused variable 'abort' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'constrain': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:306: warning: unused variable 'vstor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:304: warning: unused variable 'ncons' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:303: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'init_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:955: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'inter_charge_group_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:1120: warning: unused variable 'nat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:163: warning: 'icomp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/perf_est.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/perf_est.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c: In function 'pme_load_estimate': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c:91: warning: unused variable 'fljtab' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/nsgrid.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/nsgrid.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'set_grid_sizes': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:206: warning: unused variable 'stddev' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:206: warning: unused variable 'av' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'init_grid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:361: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:361: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'grid_first': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:474: warning: unused variable 'cx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 62%] Building C object src/mdlib/CMakeFiles/md.dir/wnblist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/wnblist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 63 /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: In function 'read_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'icmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'full' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'nnbl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:136: warning: unused variable 'b2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:136: warning: unused variable 'b1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:135: warning: unused variable 'bNL' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: In function 'dump_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:234: warning: unused variable 'buf' [ 63%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mvxvf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mvxvf.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/pme_pp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pme_pp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme_pp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 63%] [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ewald.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c Building C object src/mdlib/CMakeFiles/md.dir/edsam.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/edsam.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/edsam.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/qm_gamess.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_gamess.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_gamess.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_xml.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_qhop_xml.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c: In function 'init_ewald_tab': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c:105: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'qhop_process_attr': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:182: warning: unused variable 'eprop' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'qhop_process_tree': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:247: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'gmx_qhops_read': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:279: warning: unused variable 'npd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:279: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'add_xml_qhop': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:311: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:310: warning: unused variable 'comp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:310: warning: unused variable 'grandchild' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'gmx_qhops_write': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:333: warning: unused variable 'nmt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftpack.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftpack.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftpack.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 63%] Building C object src/mdlib/CMakeFiles/md.dir/csettle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/csettle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 64 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 64%] [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_network.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_network.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_network.c Building C object src/mdlib/CMakeFiles/md.dir/wall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/wall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'settle_proj': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:189: warning: unused variable 'kfacHH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:189: warning: unused variable 'kfacOH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:188: warning: unused variable 'invvscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:187: warning: unused variable 'derpm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'xshake': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:305: warning: unused variable 'conv' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'csettle': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:417: warning: unused variable 'shakeret' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c: In function 'do_walls': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c:109: warning: unused variable 'Heps' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/genborn.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'init_gb_still': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'rbc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'rab' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'cosine' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'factor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p3' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:205: warning: unused variable 'rk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:205: warning: unused variable 'r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:204: warning: unused variable 'angle' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:204: warning: unused variable 'length' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:202: warning: unused variable 'ibm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:202: warning: unused variable 'iam' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'at' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'idx2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'id' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'ic' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nang' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nbond' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'init_gb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:390: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'ai' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_still': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:518: warning: unused variable 'dr4' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:518: warning: unused variable 'dr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:515: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_hct': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:656: warning: unused variable 'duij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:652: warning: unused variable 'gpi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:649: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:649: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_obc': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:875: warning: unused variable 'duij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:872: warning: unused variable 'min_rad' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:872: warning: unused variable 'rad' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:871: warning: unused variable 'gpi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:868: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:868: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1094: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'gb_bonds_tab': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1346: warning: unused variable 'dvdaj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1346: warning: unused variable 'vcoul' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1339: warning: unused variable 'type' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_nonpolar': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1477: warning: unused variable 'rbi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_chainrule': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1550: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1548: warning: unused variable 'rinv11' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1547: warning: unused variable 'rsq11' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1546: warning: unused variable 'rb2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1546: warning: unused variable 'fij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_forces': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1663: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1661: warning: unused variable 'v' [ 64%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'make_gb_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1887: warning: unused variable 'apa' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'l' Building C object src/mdlib/CMakeFiles/md.dir/forcerec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/forcerec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1875: warning: 'compare_int' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'check_solvent_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:164: warning: unused variable 'excl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'set_avcsixtwelve': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:769: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'init_forcerec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1299: warning: unused variable 'ngrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1299: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1235: warning: 'forcerec_check_sse2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin_bar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdebin_bar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin_bar.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin_bar.c:99: warning: 'mde_delta_h_free' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/init.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/init.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c: In function 'set_state_entries': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c:73: warning: unused variable 'nnhpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c:64: warning: 'int_title' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_con.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_con.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: In function 'dd_make_local_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c:950: warning: unused variable 'gat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: In function 'init_domdec_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c:1074: warning: unused variable 'dc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 65 [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/nlistheuristics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/nlistheuristics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nlistheuristics.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/clincs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/clincs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: In function 'do_lincsp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'lam' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'wfac' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'rlen' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: In function 'constrain_lincs': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:1165: warning: unused variable 'error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:1114: warning: 'dump_conf' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/tgroup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tgroup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/pull.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pull.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: In function 'init_grptcstat': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c:56: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: In function 'sum_ekin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c:204: warning: unused variable 'ek' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: In function 'get_pullgrps_dr': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:301: warning: unused variable 'pref' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: In function 'do_constraint': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:458: warning: unused variable 'mass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:457: warning: unused variable 'd0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/calcvir.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_parm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_qhop_parm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_parm.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c:46: warning: 'dprod1' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c:159: warning: 'lo_fcv2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcmu.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/calcmu.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcmu.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/groupcoord.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/groupcoord.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/groupcoord.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 66 [ 66%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/stat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/stat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/stat.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: In function 'setup_gb_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:119: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:116: warning: unused variable 'nj1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:116: warning: unused variable 'nj0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:114: warning: unused variable 'tp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: In function 'genborn_allvsall_setup': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:330: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/update.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/update.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'print_missing_interactions_mb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:114: warning: unused variable 'a_gl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:114: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'global_atomnr_to_moltype_ind': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:364: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'count_excls': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:379: warning: unused variable 'n_inter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_make_reverse_top': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:628: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:628: warning: unused variable 'n_recursive_vsite' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'add_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:772: warning: unused variable 'iatoms_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'make_local_exclusions': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1234: warning: unused variable 'a_loc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_make_local_top': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1422: warning: unused variable 'bUniqueExcl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_init_local_state': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1576: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1576: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'check_link': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1616: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'do_update_vv_vel': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vnrel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'va' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vv' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vn' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'u' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:237: warning: unused variable 'vrel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:236: warning: unused variable 'gt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:235: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'do_update_vv_pos': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:287: warning: unused variable 'w_dt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:287: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_tcouple': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'homenr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1303: warning: unused variable 'vbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1298: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1298: warning: unused variable 'bExtended' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_box': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1470: warning: unused variable 'vir_con' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1469: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1468: warning: unused variable 'dt_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bEner' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bLog' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bLastStep' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_coords': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xprimein' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xpall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'fall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'forcein' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xcom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vcom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1587: warning: unused variable 'vir_con' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1586: warning: unused variable 'icom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nexpand' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nconstr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nsettle' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nshake' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'jatom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'iatom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'blen1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'blen0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1581: warning: unused variable 'imassin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1581: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bEner' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bLog' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bLastStep' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/domdec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_move_cellx': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:982: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:982: warning: unused variable 'dim1' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_collect_vec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1432: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'a' [ 66%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1430: warning: unused variable 'ma' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_distribute_vec_scatterv': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1667: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_distribute_state': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1709: warning: unused variable 'ngtcp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1709: warning: unused variable 'ngtch' Building C object src/mdlib/CMakeFiles/md.dir/domdec_setup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_setup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'gmx_ddcoord2pmeindex': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2075: warning: unused variable 'nc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2075: warning: unused variable 'coords_pme' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'make_dd_indices': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2393: warning: unused variable 'ga2la' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'check_bLocalCG': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2449: warning: unused variable 'ncg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'set_dd_cell_sizes_dlb_root': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3183: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'distribute_dd_cell_sizes_dlb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3365: warning: unused variable 'dim1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'distribute_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3657: warning: unused variable 'bUnbounded' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3653: warning: unused variable 'box_size' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3651: warning: unused variable 'npbcdim' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_redistribute_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4177: warning: unused variable 'cell_d' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4177: warning: unused variable 'd4' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'get_load_distribution': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4849: warning: unused variable 'cid' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'setup_dd_grid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:5309: warning: unused variable 'bZYX' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'check_dlb_support': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6039: warning: unused variable 'dd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'init_domain_decomposition': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_init_bondeds': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6694: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6693: warning: unused variable 'bBondComm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'guess_npme': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:145: warning: unused variable 'ir_try' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:144: warning: unused variable 'nky' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:144: warning: unused variable 'nkx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'comm_cost_est': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:298: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'assign_factors': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:486: warning: unused variable 'z' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'setup_dd_communication': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'inv_ncg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r2inc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_scomm2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_mb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_partition_system': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:8178: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:291: warning: 'ga2la_get_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 66%] Building C object src/mdlib/CMakeFiles/md.dir/ghat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ghat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ghat.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 67 [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tables.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/pullutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pullutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'done_tabledata': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:483: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'make_tables': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:868: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'make_gb_table': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:991: warning: unused variable 'x0_r2_error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:991: warning: unused variable 'x0_r_error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:990: warning: unused variable 'rel_error_r2_old' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:990: warning: unused variable 'rel_error_r_old' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:989: warning: unused variable 'rel_error_r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:989: warning: unused variable 'rel_error_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:988: warning: unused variable 'abs_error_r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:988: warning: unused variable 'abs_error_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'tabsel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:977: warning: unused variable 'fns14' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:159: warning: 'splint' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: In function 'pull_set_pbcatom': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c:85: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: In function 'pull_calc_coms': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c:281: warning: unused variable 'xx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/ns.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ns.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'init_neighbor_list': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:248: warning: unused variable 'solvent' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'new_i_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'nshift' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'put_in_list_at': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:640: warning: unused variable 'rlj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:640: warning: unused variable 'qq' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:635: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:633: warning: unused variable 'ind_ij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_inner_tric': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1466: warning: unused variable 'nsbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_inner_rect': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1499: warning: unused variable 'nsbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_simple_core': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'i0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'jcg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'nsgrid_core': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1949: warning: unused variable 'xi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1945: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'init_ns': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2402: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'search_neighbours': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2528: warning: unused variable 'cg_end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2528: warning: unused variable 'cg_start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2527: warning: unused variable 'i_egp_flags' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2526: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2522: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2522: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1637: warning: 'get_dx' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/qm_gaussian.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_gaussian.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_gaussian.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/tpi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tpi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c: In function 'do_tpi': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:160: warning: unused variable 'dvdl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:150: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:150: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:135: warning: unused variable 'TPI' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 67%] Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_mopac.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_mopac.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 68 [ 68%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_wallcycle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_wallcycle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_wallcycle.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 68%] Building C object src/mdlib/CMakeFiles/md.dir/pme.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pme.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'pmeredist_pd': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:399: warning: unused variable 'idxa' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'copy_pmegrid_to_fftgrid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:851: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'copy_fftgrid_to_pmegrid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:917: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'spread_q_bsplines': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1105: warning: unused variable 'bndsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1105: warning: unused variable 'localsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1100: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1099: warning: unused variable 'ol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'init_atomcomm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 'nk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'init_overlap_comm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1854: warning: unused variable 'nk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1854: warning: unused variable 'nn' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1853: warning: unused variable 'exten' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'maxlr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'rbnd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'lbnd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'gmx_pme_init': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2039: warning: unused variable 'atc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'gmx_pme_do': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2468: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2464: warning: unused variable 'local_ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'nz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'nx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2004: warning: 'gmx_pme_check_grid_restrictions' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 68%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_single.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_sse2_single.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_sse2_single.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 68%] Building C object src/mdlib/CMakeFiles/md.dir/force.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/gcc -Dmd_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/force.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: In function 'ns': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:86: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: In function 'do_force_lowlevel': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:147: warning: unused variable 'dvdgb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:141: warning: unused variable 'bDoEpot' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Linking C shared library libmd_d.so cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /usr/bin/gcc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libmd_d.so.6 -o libmd_d.so.6 CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/iteratedconstraints.c.o CMakeFiles/md.dir/gmx_fft_fftw2.c.o CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/domdec_box.c.o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/pppm.c.o CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/minimize.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/constr.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/nsgrid.c.o CMakeFiles/md.dir/wnblist.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/ewald.c.o CMakeFiles/md.dir/edsam.c.o CMakeFiles/md.dir/qm_gamess.c.o CMakeFiles/md.dir/gmx_qhop_xml.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/wall.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/forcerec.c.o CMakeFiles/md.dir/mdebin_bar.c.o CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/calcvir.c.o CMakeFiles/md.dir/gmx_qhop_parm.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/update.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/ghat.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/pullutil.c.o CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/force.c.o ../gmxlib/libgmx_d.so.6 -ldl -lm -lfftw3 -lxml2 -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib && /usr/bin/cmake -E cmake_symlink_library libmd_d.so.6 libmd_d.so.6 libmd_d.so make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 59 60 61 62 63 64 65 66 67 68 [ 68%] Built target md make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/depend make -f src/tools/CMakeFiles/gmxana.dir/build.make src/tools/CMakeFiles/gmxana.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/gmxana.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxpreprocess.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/gmxana.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/gmxana.dir/depend.internal". Scanning dependencies of target gmxpreprocess make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 68%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 68%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/add_par.c.o [ 68%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/add_par.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/add_par.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/compute_io.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/compute_io.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/convparm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/convparm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c: In function 'compute_io': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c:61: warning: unused variable 'nfep' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'assign_param': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:96: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'new_interaction_list': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:459: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'convert_params': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:469: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:457: warning: 'new_interaction_list' defined but not used [ 68%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gen_ad.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gen_ad.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c Scanning dependencies of target gmxana make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/gmxana.dir/build.make src/tools/CMakeFiles/gmxana.dir/build /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 68%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'get_impropers': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:437: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:436: warning: unused variable 'hbidih' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:434: warning: unused variable 'a0' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'clean_excls': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:576: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:576: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'generate_excls': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'e' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'l1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'k1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'j1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:114: warning: 'aeq' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:289: warning: 'ideq' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:327: warning: 'dump_param' defined but not used make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 68%] Building C object src/tools/CMakeFiles/gmxana.dir/autocorr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/autocorr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/autocorr.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'read_vsite_database': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:150: warning: unused variable 'prevdir' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:150: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'add_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:487: warning: unused variable 'bb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'gen_vsites_trp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:759: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:758: warning: unused variable 'mtot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:758: warning: unused variable 'mwtot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:756: warning: unused variable 'xM' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:747: warning: unused variable 'dist' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:746: warning: unused variable 'I' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'gen_vsites_tyr': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:986: warning: unused variable 'vmass' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'do_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:1350: warning: unused variable 'bb' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used [ 68%] /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/tools/CMakeFiles/gmxana.dir/expfit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/expfit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/expfit.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/expfit.c:90: warning: 'signum' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 68%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/genhydro.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/genhydro.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'expand_hackblocks_one': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:161: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'check_atoms_present': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:275: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'add_h_low': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:390: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 86 [ 69%] Building C object src/tools/CMakeFiles/gmxana.dir/polynomials.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/polynomials.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/polynomials.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 69%] Building C object src/tools/CMakeFiles/gmxana.dir/levenmar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/levenmar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:78: warning: 'dvector' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:106: warning: 'dmatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:123: warning: 'imatrix1' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:141: warning: 'submatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:168: warning: 'free_dvector' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:183: warning: 'free_dmatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:191: warning: 'free_imatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:201: warning: 'free_submatrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:208: warning: 'convert_matrix' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/levenmar.c:224: warning: 'free_convert_matrix' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 69%] Building C object src/tools/CMakeFiles/gmxana.dir/anadih.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/anadih.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/anadih.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 69%] Building C object src/tools/CMakeFiles/gmxana.dir/pp2shift.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/pp2shift.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/pp2shift.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 70 [ 70%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gpp_atomtype.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 70%] Building C object src/tools/CMakeFiles/gmxana.dir/dlist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/dlist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/dlist.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 70%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gpp_bond_atomtype.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/dlist.c: In function 'mk_dlist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/dlist.c:52: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/dlist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 70%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/h_db.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/h_db.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: In function 'dump_h_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:117: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: In function 'read_h_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:200: warning: unused variable 'fp' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used [ 70%] 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/usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/hizzie.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c: In function 'set_histp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:195: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:192: warning: unused variable 'his0' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:192: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:188: warning: unused variable 'bHaveH' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 70%] Building C object src/tools/CMakeFiles/gmxana.dir/cmat.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/cmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/cmat.c [ 70%] Building C object src/tools/CMakeFiles/gmxana.dir/eigensolver.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/eigensolver.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c: In function 'eigensolver': /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c:64: warning: unused variable 'iu' /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c:64: warning: unused variable 'il' /builddir/build/BUILD/gromacs-4.5.5/src/tools/eigensolver.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 87 [ 71%] Building C object src/tools/CMakeFiles/gmxana.dir/nsc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/nsc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 71%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/nm2type.c.o [ 71%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/nm2type.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c Building C object src/tools/CMakeFiles/gmxana.dir/hxprops.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/hxprops.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/hxprops.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 71%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/pdb2top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/pdb2top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c: In function 'nsc_dclm_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c:660: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c:540: warning: unused variable 'jat_xx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/nsc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/hxprops.c: In function 'ellipticity': /builddir/build/BUILD/gromacs-4.5.5/src/tools/hxprops.c:84: warning: unused variable 'Xi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/hxprops.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: In function 'rd_nm2type_file': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c:72: warning: unused variable 'blen' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: In function 'nm2type': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c:179: warning: unused variable 'quality' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'missing_atoms': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:85: warning: unused variable 'bRet' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'print_top_comment': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:539: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'get_hackblocks_rtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:983: warning: unused variable 'bC' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:983: warning: unused variable 'bN' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:981: warning: unused variable 'Hnum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:980: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'match_atomnames_with_rtp_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1160: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'match_atomnames_with_rtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1324: warning: unused variable 'bFoundInAdd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1323: warning: unused variable 'start_nr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1322: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1322: warning: unused variable 'start_at' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1321: warning: unused variable 'anmnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1320: warning: unused variable 'hbr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1317: warning: unused variable 'newnm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1316: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'gen_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1354: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1354: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:743: warning: 'inter_res_bond' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 71%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/pgutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/pgutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pgutil.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 71 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] [ 72%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/readir.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/readir.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c Building C object src/tools/CMakeFiles/gmxana.dir/fitahx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/fitahx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/fitahx.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'check_ir': /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:162: warning: unused variable 'ns_type' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'do_index': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:1782: warning: unused variable 'SAtime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'triple_check': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:2293: warning: unused variable 'npct' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Building C object src/tools/CMakeFiles/gmxana.dir/geminate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/geminate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: In function 'init_gemParams': /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:672: warning: statement with no effect /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: In function 'fitGemRecomb': /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:751: warning: unused variable 'dumpname' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:751: warning: unused variable 'dumpstr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:750: warning: unused variable 'GD' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:749: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:749: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:748: warning: unused variable 'dumpdata' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:748: warning: unused variable 'tol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:748: warning: unused variable 'd2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:748: warning: unused variable 'size' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'maxiter' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'iter' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:747: warning: unused variable 'nThreads' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: In function 'takeAwayBallistic': /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1019: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1018: warning: unused variable 'sorted' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1017: warning: unused variable 'ddt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1016: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1015: warning: unused variable 'A' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1014: warning: unused variable 'guess' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1013: warning: unused variable 'BD' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1012: warning: unused variable 'iter' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1012: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1012: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: In function 'fixGemACF': /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1257: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.h:5: warning: 'gemType' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:96: warning: 'gem_Re' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:97: warning: 'gem_Im' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:191: warning: 'gem_cxintpow' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:268: warning: 'gem_cxrsqrt' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:288: warning: 'gem_cxprintf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:424: warning: 'gem_W' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:434: warning: 'gem_cerf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:540: warning: 'gem_cW' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:557: warning: 'eq10v2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:611: warning: 'getLogIndex' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.c:1221: warning: 'd2r' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_analyze.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_analyze.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c: In function 'luzar_correl': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:631: warning: unused variable 'weight' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:629: warning: unused variable 'tol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c: In function 'gmx_analyze': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:1064: warning: unused variable 'gemfile' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:984: warning: unused variable 'rcut' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:984: warning: unused variable 'diffusion' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:983: warning: unused variable 'nFitPoints' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:982: warning: unused variable 'bLuzarError' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/geminate.h:5: warning: 'gemType' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:323: warning: 'anal_ee' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_analyze.c:836: warning: 'do_geminate' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_anaeig.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_anaeig.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: In function 'calc_entropy_schlitter': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:98: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:97: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:97: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:97: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:96: warning: unused variable 'indx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: In function 'compare': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:229: warning: unused variable 'nrow' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: In function 'rmsf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:717: warning: unused variable 'nrow' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: In function 'gmx_anaeig': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:860: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:859: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:859: warning: unused variable 'xid' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:857: warning: unused variable 'xread' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:857: warning: unused variable 'x' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:850: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:850: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c:849: warning: unused variable 'out' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_anaeig.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/readpull.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/readpull.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c: In function 'read_pullparams': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c:107: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c:103: warning: unused variable 'nchar' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/resall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/resall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c: In function 'read_resall': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c:256: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c:482: warning: 'neq_str' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_angle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_angle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c: In function 'gmx_g_angle': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:150: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:146: warning: unused variable 'fraction' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:146: warning: unused variable 'aa' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:146: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:141: warning: unused variable 'angind' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:141: warning: unused variable 'nat2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:141: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:141: warning: unused variable 'total' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:138: warning: unused variable 'Jc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:135: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c:134: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_angle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/sorting.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/sorting.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/sorting.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/specbond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/specbond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/specbond.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 88 [ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_bond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bond.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_bundle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c: In function 'dump_axes': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c:143: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c: In function 'gmx_bundle': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c:215: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c:211: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c:200: warning: unused variable 'out' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bundle.c: At top level: /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 73%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/gmxana.dir/gmx_chi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_chi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c [ 73%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/ter_db.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/ter_db.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'read_atom':/builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c: In function 'histogramming': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c:424: warning: unused variable 'his_aa1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:84: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'print_ter_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:136: warning: unused variable 'nname' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'filter_ter': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:375: warning: unused variable 's2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:373: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c: In function 'gmx_chi': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c:1136: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_chi.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_cluster.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_cluster.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_cluster.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 73%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/tomorse.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/tomorse.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tomorse.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_cluster.c: In function 'mark_clusters': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_cluster.c:644: warning: unused variable 'v' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_cluster.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used[ 73%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_confrms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_confrms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c: In function 'find_matching_names': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:259: warning: unused variable 'atnm2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:259: warning: unused variable 'atnm1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:259: warning: unused variable 'resnm2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:259: warning: unused variable 'resnm1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:256: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:254: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c: In function 'gmx_confrms': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:419: warning: unused variable 'tmas2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:419: warning: unused variable 'tmas1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c:416: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_confrms.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 72 [ 74%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topdirs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topdirs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topdirs.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 74%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topexcl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topexcl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c: In function 'generate_excl': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 74%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/gmxana.dir/gmx_covar.c.o [ 74%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_covar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: In function 'generate_gb_exclusion_interactions': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n14' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n13' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:389: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:389: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: In function 'read_topol': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:517: warning: unused variable 'block' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c: In function 'gmx_covar': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c:144: warning: unused variable 'count' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c:143: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c:143: warning: unused variable 'ntopatoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c:133: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_covar.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 74%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_current.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_current.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c: In function 'calc_mjdsp': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:271: warning: unused variable 'rfr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:270: warning: unused variable 'rtmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c: In function 'dielectric': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:333: warning: unused variable 'qtmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:315: warning: unused variable 'dm_d' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:315: warning: unused variable 'dm_s' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:305: warning: unused variable 'rfr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:300: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:299: warning: unused variable 'f' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:299: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:299: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c: In function 'gmx_current': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:732: warning: unused variable 'tfile' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:731: warning: unused variable 'outi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:728: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:727: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:726: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:725: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:725: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:725: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c:723: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_current.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 74%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_density.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_density.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c: In function 'calc_density': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:259: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:254: warning: unused variable 'ax2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:254: warning: unused variable 'ax1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:252: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c:251: warning: unused variable 'slCount' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_density.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 89 [ 75%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_densmap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_densmap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densmap.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/toppush.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/toppush.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_nbt': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:794: warning: unused variable 'sig6' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:792: warning: unused variable 'atnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:787: warning: unused variable 'form2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_cmaptype': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:920: warning: unused variable 'bAllowRepeat' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:915: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'default_cmap_params': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1312: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_bond': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1485: warning: unused variable 'paramB' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'param_defB' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'param_defA' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'paramB' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dih.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dih.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dih.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dielectric.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dielectric.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dih.c:56: warning: 'dump_dih' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c: In function 'calc_nbegin': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c:62: warning: unused variable 'dtt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c:62: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dielectric.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topshake.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topshake.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/toputil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/toputil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toputil.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_kinetics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_kinetics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_kinetics.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c: In function 'make_shake': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c:98: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c:98: warning: unused variable 'nb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toputil.c:175: warning: 'print_nbt' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_spatial.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_spatial.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c: In function 'gmx_spatial': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c:134: warning: unused variable 'shx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c:106: warning: unused variable 'bSHIFT' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spatial.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_block': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_blocka': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:321: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:320: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_top': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_groups': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:376: warning: unused variable 'ndiff' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'comp_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:715: warning: unused variable 'sh' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'comp_enx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:1048: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:1045: warning: unused variable 'block' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'vsitetype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_angles': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'vsitetype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_dihs': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'ftype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_tune_pme.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_tune_pme.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tune_pme.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dipoles.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dipoles.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'do_gkr': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:159: warning: unused variable 'r2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:158: warning: unused variable 'index' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'print_gkrbin': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:296: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:296: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'mol_quad': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:425: warning: unused variable 'rcom_n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:425: warning: unused variable 'rcom_m' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'compute_avercos': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:589: warning: unused variable 'n5' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:589: warning: unused variable 'dc1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'do_dip': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:916: warning: unused variable 'gi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:1196: warning: unused variable 'mm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:1187: warning: unused variable 'lsq' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'Vol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'Msq' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'Mz' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'My' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:690: warning: unused variable 'Mx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:683: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:682: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:680: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:678: warning: unused variable 'nmol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:678: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:678: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: In function 'gmx_dipoles': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:1352: warning: unused variable 'bCorr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c:1307: warning: unused variable 'bMolCorr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dipoles.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 73 [ 76%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/fflibutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/fflibutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 90 [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_disre.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_disre.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_disre.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c: In function 'low_fflib_search_file_end': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:159: warning: unused variable 'pdum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:153: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:151: warning: unused variable 'ret' [ 77%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/xlate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -Dgmxpreprocess_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/xlate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xlate.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_disre.c: In function 'dump_disre_matrix': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_disre.c:450: warning: unused variable 'iii' [ 77%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_disre.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not usedBuilding C object src/tools/CMakeFiles/gmxana.dir/gmx_dist.c.o /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not usedcd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c: In function 'gmx_dist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c:102: warning: unused variable 'fplt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c:94: warning: unused variable 'aid'Linking C shared library libgmxpreprocess_d.so /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c:88: warning: unused variable 'v' cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess.dir/link.txt --verbose=1 /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/gcc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libgmxpreprocess_d.so.6 -o libgmxpreprocess_d.so.6 CMakeFiles/gmxpreprocess.dir/add_par.c.o CMakeFiles/gmxpreprocess.dir/compute_io.c.o CMakeFiles/gmxpreprocess.dir/convparm.c.o CMakeFiles/gmxpreprocess.dir/gen_ad.c.o CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o CMakeFiles/gmxpreprocess.dir/genhydro.c.o CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o CMakeFiles/gmxpreprocess.dir/h_db.c.o CMakeFiles/gmxpreprocess.dir/hackblock.c.o CMakeFiles/gmxpreprocess.dir/hizzie.c.o CMakeFiles/gmxpreprocess.dir/nm2type.c.o CMakeFiles/gmxpreprocess.dir/pdb2top.c.o CMakeFiles/gmxpreprocess.dir/pgutil.c.o CMakeFiles/gmxpreprocess.dir/readir.c.o CMakeFiles/gmxpreprocess.dir/readpull.c.o CMakeFiles/gmxpreprocess.dir/resall.c.o CMakeFiles/gmxpreprocess.dir/sorting.c.o CMakeFiles/gmxpreprocess.dir/specbond.c.o CMakeFiles/gmxpreprocess.dir/ter_db.c.o CMakeFiles/gmxpreprocess.dir/tomorse.c.o CMakeFiles/gmxpreprocess.dir/topdirs.c.o CMakeFiles/gmxpreprocess.dir/topexcl.c.o CMakeFiles/gmxpreprocess.dir/topio.c.o CMakeFiles/gmxpreprocess.dir/toppush.c.o CMakeFiles/gmxpreprocess.dir/topshake.c.o CMakeFiles/gmxpreprocess.dir/toputil.c.o CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o CMakeFiles/gmxpreprocess.dir/fflibutil.c.o CMakeFiles/gmxpreprocess.dir/xlate.c.o ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -lpthread -ldl -lm -lfftw3 -lxml2 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dyndom.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dyndom.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_symlink_library libgmxpreprocess_d.so.6 libgmxpreprocess_d.so.6 libgmxpreprocess_d.so make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 70 71 72 73 [ 77%] Built target gmxpreprocess make -f src/kernel/CMakeFiles/g_luck.dir/build.make src/kernel/CMakeFiles/g_luck.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_luck.dir/DependInfo.cmake --color= /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c: In function 'rot_conf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:61: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:59: warning: unused variable 'temp43' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:59: warning: unused variable 'temp21' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:59: warning: unused variable 'temp4' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:58: warning: unused variable 'Tx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:58: warning: unused variable 'Tinvcm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:58: warning: unused variable 'Tcm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c:56: warning: unused variable 'center' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dyndom.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_luck.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_luck.dir/depend.internal". Scanning dependencies of target g_luck make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/g_luck.dir/build.make src/kernel/CMakeFiles/g_luck.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 77%] Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_luck.dir/g_luck.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_luck.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_enemat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_enemat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_enemat.c /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used make -f src/kernel/CMakeFiles/g_protonate.dir/build.make src/kernel/CMakeFiles/g_protonate.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_protonate.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_protonate.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_protonate.dir/depend.internal". Linking C executable g_luck_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_luck.dir/link.txt --verbose=1 Scanning dependencies of target g_protonate make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/g_protonate.dir/build.make src/kernel/CMakeFiles/g_protonate.dir/build /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_luck.dir/g_luck.c.o -o g_luck_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 77%] Building C object src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_protonate.dir/g_protonate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_protonate.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 77%] Built target g_luck make -f src/kernel/CMakeFiles/g_x2top.dir/build.make src/kernel/CMakeFiles/g_x2top.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_x2top.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_x2top.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_x2top.dir/depend.internal". Scanning dependencies of target g_x2top make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/g_x2top.dir/build.make src/kernel/CMakeFiles/g_x2top.dir/build /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 77%] Building C object src/kernel/CMakeFiles/g_x2top.dir/g_x2top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_x2top.dir/g_x2top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c Linking C executable g_protonate_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_protonate.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_protonate.dir/g_protonate.c.o -o g_protonate_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c: In function 'set_cgnr': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:177: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c: In function 'set_force_const': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:254: warning: unused variable 'i' make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:425: warning: unused variable 'scale' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:415: warning: unused variable 'cutoff' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'ndih' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:411: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:410: warning: unused variable 'nres' [ 77%] Built target g_protonate make -f src/kernel/CMakeFiles/gmxcheck.dir/build.make src/kernel/CMakeFiles/gmxcheck.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxcheck.dir/DependInfo.cmake --color= /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxcheck.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxcheck.dir/depend.internal". /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:79: warning: 'set_x_blen' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/g_x2top.c:116: warning: 'get_atype' defined but not used Scanning dependencies of target gmxcheck make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/gmxcheck.dir/build.make src/kernel/CMakeFiles/gmxcheck.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 77%] Building C object src/kernel/CMakeFiles/gmxcheck.dir/gmxcheck.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxcheck.dir/gmxcheck.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_energy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_energy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'tpx2system': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:89: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'tpx2methods': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:135: warning: unused variable 'sh' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'chk_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:198: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'chk_trj': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:249: warning: unused variable 'bOK' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:248: warning: unused variable 'prec' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:248: warning: unused variable 'tt' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:248: warning: unused variable 'rdum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'chk_ndx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:523: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: In function 'chk_enx': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'select_by_name': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:160: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c:547: warning: unused variable 'ndr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'calc_averages': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:600: warning: unused variable 'steps' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'remove_drift':/builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxcheck.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:848: warning: unused variable 'sd2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:848: warning: unused variable 'sd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:848: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'calc_fluctuation_props': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:880: warning: unused variable 'vv2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:880: warning: unused variable 'hh2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'analyse_ener': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1032: warning: unused variable 'chi2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1031: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1030: warning: unused variable 'x1mk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1030: warning: unused variable 'x1m' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'fstep' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'diffav' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'diffsum' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'oldfrac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1026: warning: unused variable 'sfrac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1025: warning: unused variable 'xxx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'fec': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1279: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1279: warning: unused variable 'nre' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: In function 'gmx_energy': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1802: warning: unused variable 'nms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1795: warning: unused variable 'ener' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1794: warning: unused variable 'bEDR' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1780: warning: unused variable 'ee' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:1774: warning: unused variable 'drout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_energy.c:139: warning: 'strcount' defined but not used make -f src/kernel/CMakeFiles/gmxdump.dir/build.make src/kernel/CMakeFiles/gmxdump.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxdump.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxdump.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxdump.dir/depend.internal". Scanning dependencies of target gmxdump make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/gmxdump.dir/build.make src/kernel/CMakeFiles/gmxdump.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 69 [ 78%] Building C object src/kernel/CMakeFiles/gmxdump.dir/gmxdump.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxdump.dir/gmxdump.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c: In function 'list_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:150: warning: left-hand operand of comma expression has no effect /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:99: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c: In function 'list_ene': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:326: warning: unused variable 'rav' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:320: warning: unused variable 'ndr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gmxdump.c:64: warning: 'dump_top' defined but not used Linking C executable g_x2top_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_x2top.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_x2top.dir/g_x2top.c.o -o g_x2top_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 78%] Built target g_x2top make -f src/kernel/CMakeFiles/grompp.dir/build.make src/kernel/CMakeFiles/grompp.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/grompp.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/grompp.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/grompp.dir/depend.internal". Scanning dependencies of target grompp make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/grompp.dir/build.make src/kernel/CMakeFiles/grompp.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 78%] Building C object src/kernel/CMakeFiles/grompp.dir/grompp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/grompp.dir/grompp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: In function 'read_posres': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:712: warning: unused variable 'bFirst' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: In function 'gen_posres': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:839: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:839: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: In function 'init_cmap_grid': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1012: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1249: warning: unused variable 'born' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1248: warning: unused variable 'gb_plist' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1247: warning: unused variable 'n14' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1247: warning: unused variable 'n13' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1247: warning: unused variable 'n12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c:1236: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/grompp.c: At top level: Linking C executable gmxcheck_d /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxcheck.dir/link.txt --verbose=1 /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used/usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/gmxcheck.dir/gmxcheck.c.o -o gmxcheck_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable gmxdump_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxdump.dir/link.txt --verbose=1 [ 78%] Built target gmxcheck make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/gmxdump.dir/gmxdump.c.o -o gmxdump_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/mdrun.dir/depend.internal". make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 69 Scanning dependencies of target mdrun [ 78%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/build Built target gmxdump make -f src/kernel/CMakeFiles/pdb2gmx.dir/build.make src/kernel/CMakeFiles/pdb2gmx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/pdb2gmx.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/pdb2gmx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/pdb2gmx.dir/depend.internal". /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 78%] Building C object src/kernel/CMakeFiles/mdrun.dir/gctio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/gctio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gctio.c Scanning dependencies of target pdb2gmx make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/pdb2gmx.dir/build.make src/kernel/CMakeFiles/pdb2gmx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 75 [ 79%] Building C object src/kernel/CMakeFiles/pdb2gmx.dir/pdb2gmx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/pdb2gmx.dir/pdb2gmx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c: In function 'rename_resrtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:296: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c: In function 'sort_pdbatoms': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:615: warning: unused variable 'hbr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:1164: warning: unused variable 'bCheckMerge' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:1154: warning: unused variable 'rtp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2gmx.c:180: warning: 'get_cystp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 79%] Building C object src/kernel/CMakeFiles/mdrun.dir/ionize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/ionize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ionize.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 79%] Building C object src/kernel/CMakeFiles/mdrun.dir/runner.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/runner.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c: In function 'mdrunner': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:362: warning: unused variable 'list' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:359: warning: unused variable 'gro' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:348: warning: unused variable 'tmpr2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:348: warning: unused variable 'tmpr1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:342: warning: unused variable 'realtime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:342: warning: unused variable 'nodetime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used Linking C executable grompp_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/grompp.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/grompp.dir/grompp.c.o -o grompp_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 79%] Built target grompp /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 74 [ 79%] [ 80%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_lie.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_lie.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_lie.c Building C object src/kernel/CMakeFiles/mdrun.dir/do_gct.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/do_gct.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: In function 'init_coupling': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:62: warning: unused variable 'atj' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:62: warning: unused variable 'ati' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'index' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'nc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: In function 'do_coupling': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:493: warning: unused variable 'bTest' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:491: warning: unused variable 'xi12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:491: warning: unused variable 'xi6' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffa' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:489: warning: unused variable 'rmsf' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:461: warning: 'dump_fm' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 80%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_filter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_filter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_filter.c Linking C executable pdb2gmx_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx.dir/link.txt --verbose=1 /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/pdb2gmx.dir/pdb2gmx.c.o -o pdb2gmx_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 75 [ 80%] Built target pdb2gmx /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 80%] Building C object src/kernel/CMakeFiles/mdrun.dir/repl_ex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/repl_ex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 80%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: In function 'init_replica_exchange': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:118: warning: unused variable 'temp' Building C object src/tools/CMakeFiles/gmxana.dir/gmx_gyrate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_gyrate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_gyrate.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: In function 'replica_exchange': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:725: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:706: warning: 'write_debug_x' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_gyrate.c: In function 'gmx_gyrate': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_gyrate.c:191: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_gyrate.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used make -f src/kernel/CMakeFiles/tpbconv.dir/build.make src/kernel/CMakeFiles/tpbconv.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/tpbconv.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/tpbconv.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/tpbconv.dir/depend.internal". Scanning dependencies of target tpbconv make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/tpbconv.dir/build.make src/kernel/CMakeFiles/tpbconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 80%] Building C object src/kernel/CMakeFiles/tpbconv.dir/tpbconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/tpbconv.dir/tpbconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c:374: warning: unused variable 'nerror' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c:333: warning: unused variable 'gopts' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c:332: warning: unused variable 'irnew' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbconv.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 91 [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_h2order.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_h2order.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_h2order.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used Building C object src/kernel/CMakeFiles/mdrun.dir/xutils.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/xutils.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/md.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/md.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c: In function 'update_forcefield': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c:334: warning: unused variable 'bDone' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c: In function 'do_md': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:184: warning: unused variable 'iter_i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:179: warning: unused variable 'oldfom' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:179: warning: unused variable 'fom' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:178: warning: unused variable 'tmpvir' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:174: warning: unused variable 'grpname' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:164: warning: unused variable 'timestep' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:140: warning: unused variable 'ebox' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:140: warning: unused variable 'scale_tot' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_hbond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_hbond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'findMirror': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:584: warning: unused variable 'u' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'add_frames': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:601: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:601: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:601: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:601: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'search_donors': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1040: warning: unused variable 'stop' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1036: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1036: warning: unused variable 'nra' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'is_hbond': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1471: warning: unused variable 'ihb' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'do_merge': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1593: warning: unused variable 'pShift' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'merge_hb': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1674: warning: unused variable 'ogrp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1674: warning: unused variable 'grp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1674: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'do_nhb_dist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1736: warning: unused variable 'nhb' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'smooth_tail': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2102: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'analyse_corr': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2125: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2125: warning: unused variable 'dgp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2125: warning: unused variable 'dg' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'do_hbac': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2297: warning: unused variable 'fittolerance' Linking C executable tpbconv_d /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2295: warning: unused variable 'E' cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/tpbconv.dir/link.txt --verbose=1 /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2293: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2291: warning: unused variable 'ptimes' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2283: warning: unused variable 'ght_fac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2283: warning: unused variable 'ct_fac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2283: warning: unused variable 'p_ct' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2281: warning: unused variable 'nhbi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2271: warning: unused variable 'legNN' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2270: warning: unused variable 'iter' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2270: warning: unused variable 'nd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2270: warning: unused variable 'o' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2270: warning: unused variable 'n'/usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/tpbconv.dir/tpbconv.c.o -o tpbconv_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: In function 'gmx_hbond': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:4007: warning: unused variable 'rtmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:4006: warning: unused variable 'itmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3259: warning: unused variable 'threadNr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3258: warning: unused variable 'actual_nThreads' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3258: warning: unused variable 'jj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3257: warning: unused variable 'E' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3251: warning: unused variable 'kcell' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3249: warning: unused variable 'fpins' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3246: warning: unused variable 'bin' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3244: warning: unused variable 'was' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'zkk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'ykk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'xkk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'ak' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'zk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'yk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3243: warning: unused variable 'xk' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'ja' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'id' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3240: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3153: warning: unused variable 'NNtype' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:3152: warning: unused variable 'logAfterTime' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:899: warning: 'in_list' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1159: warning: 'control_pHist' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:1431: warning: 'pbc_correct' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hbond.c:2229: warning: 'parallel_print' defined but not used make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Built target tpbconv /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_helix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_helix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helix.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_mindist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_mindist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helix.c: In function 'gmx_helix': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helix.c:215: warning: unused variable 'nre' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helix.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c: In function 'periodic_mindist_plot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:116: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c: In function 'dist_plot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:273: warning: unused variable 'frout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c: In function 'gmx_mindist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:543: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:542: warning: unused variable 'atm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:537: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c:502: warning: unused variable 'bugs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mindist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/mdrun.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/mdrun.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:551: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:503: warning: unused variable 'fptest' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:498: warning: unused variable 'ed' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:387: warning: unused variable 'bPPPME' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:386: warning: unused variable 'bCart' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/genalg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/genalg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_msd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_msd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_msd.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c: In function 'update_ga': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c:196: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_msd.c:163: warning: 'done_corr' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/md_openmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c: In function 'do_md_openmm': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c:151: warning: unused variable 'reset_counters_now' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c:151: warning: unused variable 'reset_counters' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_morph.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_morph.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_morph.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Linking C executable mdrun_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/mdrun.dir/gctio.c.o CMakeFiles/mdrun.dir/ionize.c.o CMakeFiles/mdrun.dir/runner.c.o CMakeFiles/mdrun.dir/do_gct.c.o CMakeFiles/mdrun.dir/repl_ex.c.o CMakeFiles/mdrun.dir/xutils.c.o CMakeFiles/mdrun.dir/md.c.o CMakeFiles/mdrun.dir/mdrun.c.o CMakeFiles/mdrun.dir/genalg.c.o CMakeFiles/mdrun.dir/md_openmm.c.o -o mdrun_d -rdynamic -ldl -lm libgmxpreprocess_d.so.6 ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread -lfftw3 -lxml2 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 81%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_nmeig.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_nmeig.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 74 [ 81%] Built target mdrun /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 92 [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_nmens.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_nmens.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c: In function 'nma_full_hessian': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:144: warning: unused variable 'rdum' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c: In function 'gmx_nmeig': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:318: warning: unused variable 'index' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:316: warning: unused variable 'gnx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:316: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:316: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:315: warning: unused variable 'grpname' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:314: warning: unused variable 'count' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:313: warning: unused variable 'mass_fac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:313: warning: unused variable 'rdum' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:308: warning: unused variable 'ePBC' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:305: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c:305: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmeig.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c: In function 'gmx_nmens': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:107: warning: unused variable 'eigvalnr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:106: warning: unused variable 'invfr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:100: warning: unused variable 'neigval' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:99: warning: unused variable 'totmass' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:90: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c:90: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmens.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_order.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_order.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c: In function 'find_nearest_neighbours': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:91: warning: unused variable 'nnb' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:90: warning: unused variable 'mm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:90: warning: unused variable 'm1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:89: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:88: warning: unused variable 'dmat' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:85: warning: unused variable 'dx2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:85: warning: unused variable 'dx1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:84: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:84: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:82: warning: unused variable 'fnsgdist' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:81: warning: unused variable 'fpoutdist' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c: In function 'calc_tetra_order_parm': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:240: warning: unused variable 'subtitle' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:240: warning: unused variable 'fn' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c: In function 'calc_order': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:371: warning: unused variable 'dbangle' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c:367: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_order.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_principal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_principal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_polystat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_polystat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_polystat.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c: In function 'gmx_principal': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:98: warning: unused variable 'a3' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:98: warning: unused variable 'a2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:98: warning: unused variable 'a1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'mol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'nam' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c:96: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_principal.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_polystat.c: In function 'calc_int_dist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_polystat.c:82: warning: unused variable 'jj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_polystat.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_potential.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_potential.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c: In function 'calc_potential': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c:115: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c:114: warning: unused variable 'slCount' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_potential.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rama.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rama.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rama.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 82%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rdf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rdf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 93 [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rms.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rmsf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rmsf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c: In function 'do_rdf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'mol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:195: warning: unused variable 'cur' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:190: warning: unused variable 'mols' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:174: warning: unused variable 'index_cm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:173: warning: unused variable 'isize_cm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:170: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:170: warning: unused variable 'j1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:170: warning: unused variable 'j0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:168: warning: unused variable 'outf2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c:168: warning: unused variable 'outf1' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rdf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c: In function 'gmx_rmsf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:217: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:216: warning: unused variable 'res0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:211: warning: unused variable 'bCont' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:207: warning: unused variable 'ir' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:206: warning: unused variable 'header' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:204: warning: unused variable 'w_rms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:204: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:203: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:203: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:203: warning: unused variable 'nre' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:203: warning: unused variable 'step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c:193: warning: unused variable 'bdevX' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rotacf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rotacf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rotacf.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_saltbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_saltbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c: In function 'gmx_saltbr': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:170: warning: unused variable 'label' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:169: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:169: warning: unused variable 't0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:163: warning: unused variable 'n3' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:163: warning: unused variable 'n2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c:163: warning: unused variable 'n1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_saltbr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_sas.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_sas.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sas.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_select.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_select.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_select.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sas.c: In function 'sas_plot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sas.c:382: warning: unused variable 'mm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sas.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_select.c: In function 'gmx_select': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_select.c:255: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_select.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rmsdist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rmsdist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c: In function 'analyze_noe_equivalent': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c:250: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c: In function 'gmx_rmsdist': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c:535: warning: unused variable 'gj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c:535: warning: unused variable 'gi' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c:535: warning: unused variable 'j' [ 83%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rmsdist.c: At top level: Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rotmat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_rotmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_rotmat.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 94 [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_sgangle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_sgangle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sgangle.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_sorient.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_sorient.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_spol.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_spol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c: In function 'gmx_sorient': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c:115: warning: unused variable 'mtot' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c:115: warning: unused variable 'mass' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c:109: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sorient.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c: In function 'gmx_spol': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c:169: warning: unused variable 'bPBC' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c:132: warning: unused variable 'xtop' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c:128: warning: unused variable 'title' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_spol.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_tcaf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_tcaf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_traj.c.o /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c: In function 'gmx_tcaf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c:278: warning: unused variable 'c1' cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_traj.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c:268: warning: unused variable 'bTPS' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_tcaf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_velacc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_velacc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_velacc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_helixorient.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_helixorient.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c: In function 'write_pdb_bfac': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c:429: warning: unused variable 'bOne' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c: In function 'gmx_traj': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c:672: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_traj.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c: In function 'gmx_helixorient': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:126: warning: unused variable 'rotangle' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:108: warning: unused variable 'axes' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:107: warning: unused variable 'axes_t0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:94: warning: unused variable 'vproj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:94: warning: unused variable 'vtmp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:94: warning: unused variable 'p2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:94: warning: unused variable 'p1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:93: warning: unused variable 'averageaxis' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:87: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c:81: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_helixorient.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 95 [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_clustsize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_clustsize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_mdmat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_mdmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c: In function 'clust_size': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:97: warning: unused variable 'n_y' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:97: warning: unused variable 'ak' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:92: warning: unused variable 'nsame' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c: In function 'gmx_clustsize': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:407: warning: unused variable 'bRDF' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c:407: warning: unused variable 'bSQ' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_clustsize.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c: In function 'gmx_mdmat': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c:194: warning: unused variable 'nr0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c:192: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c:165: warning: unused variable 'bAtom' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_mdmat.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_wham.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_wham.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_wham.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/correl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/correl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/correl.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/correl.c: In function 'complex_mult': /builddir/build/BUILD/gromacs-4.5.5/src/tools/correl.c:188: warning: unused variable 'no2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/correl.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_sham.c.o /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_sham.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_nmtraj.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_nmtraj.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c: In function 'do_sham': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:288: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c: In function 'gmx_sham': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'db' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'cum4' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'cum3' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'cum2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'cum1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'sig' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:778: warning: unused variable 'av' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:776: warning: unused variable 'error' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:776: warning: unused variable 'tot' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:775: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:775: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:775: warning: unused variable 'nlast' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:774: warning: unused variable 'out' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:728: warning: unused variable 'resol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:728: warning: unused variable 'nb_min' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:723: warning: unused variable 'bShamEner' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:722: warning: unused variable 'bPower' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:722: warning: unused variable 'bEeFitAc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:722: warning: unused variable 'bEENLC' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:722: warning: unused variable 'bEESEF' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:721: warning: unused variable 'bXYdy' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:721: warning: unused variable 'bAverCorr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:721: warning: unused variable 'bSubAv' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:720: warning: unused variable 'filtlen' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c:720: warning: unused variable 'frac' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_sham.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c: In function 'gmx_nmtraj': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:124: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:123: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:121: warning: unused variable 'out_eigval' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:115: warning: unused variable 'neigval' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:113: warning: unused variable 'grpname' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:111: warning: unused variable 'indexfile' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:109: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:109: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c:105: warning: unused variable 'eigvalnr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_nmtraj.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_trjconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_trjconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_trjcat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_trjcat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c: In function 'calc_pbc_cluster': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:111: warning: unused variable 'com_dist2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c: In function 'put_molecule_com_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:282: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c: In function 'gmx_trjconv': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:826: warning: unused variable 'xdr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:825: warning: unused variable 'command' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:803: warning: unused variable 'gn_rms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:802: warning: unused variable 'ind_rms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:801: warning: unused variable 'irms' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:790: warning: unused variable 'nre' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:789: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:789: warning: unused variable 'xtcpr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:788: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:788: warning: unused variable 'box_center' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c: In function 'scan_trj_files': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:81: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c: In function 'gmx_trjcat': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:464: warning: unused variable 'last_ok_step' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:460: warning: unused variable 'in_file' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:457: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:457: warning: unused variable 'x' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:455: warning: unused variable 'trjout' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c:455: warning: unused variable 'ftpin' /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c:72: warning: 'sort_comdist2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjcat.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 96 [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_trjorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_trjorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjorder.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_xpm2ps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_xpm2ps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'xpm_mat': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:570: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:570: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:569: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'tick_spacing': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:610: warning: unused variable 'bFive' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'ps_mat': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:655: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'write_combined_matrix': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:931: warning: unused variable 'map' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: In function 'gmx_xpm2ps': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c:1146: warning: unused variable 'bAdd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_xpm2ps.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used [ 86%] /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used Building C object src/tools/CMakeFiles/gmxana.dir/gmx_editconf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_editconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c: In function 'calc_geom': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:109: warning: unused variable 'grpnames' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c: In function 'set_pdb_conf_bfac': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:212: warning: unused variable 'out' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c: In function 'gmx_editconf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'zcent' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'ycent' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'xcent' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'zs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'ys' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:673: warning: unused variable 'xs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:671: warning: unused variable 'bCubic' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:666: warning: unused variable 'tindex' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:665: warning: unused variable 'tsize' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:563: warning: unused variable 'to_diam' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:563: warning: unused variable 'rbox' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_editconf.c:82: warning: 'pdbtp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_genbox.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_genbox.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genbox.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genbox.c: In function 'gmx_genbox': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genbox.c:694: warning: unused variable 'pbc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genbox.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_genion.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_genion.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c: In function 'insert_ion': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:72: warning: unused variable 'xei' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:70: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:70: warning: unused variable 'wlast' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:70: warning: unused variable 'owater' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c: In function 'update_topol': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c:236: warning: unused variable 'nsol' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genion.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_genconf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_genconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genconf.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genconf.c:93: warning: 'move_x' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 86%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_genpr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_genpr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_genpr.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 97 /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_eneconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_eneconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c: In function 'scan_ene_files': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:148: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c: In function 'gmx_eneconv': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:499: warning: unused variable 'ok' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:498: warning: unused variable 'buf3' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:498: warning: unused variable 'chptr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:498: warning: unused variable 'inputstring' [ 87%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:497: warning: unused variable 't1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:494: warning: unused variable 'j' Building C object src/tools/CMakeFiles/gmxana.dir/gmx_vanhove.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_vanhove.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_vanhove.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:102: warning: 'same_time' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:318: warning: 'remove_last_eeframe' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_eneconv.c:386: warning: 'update_last_ee' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 87%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/gmxana.dir/gmx_wheel.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_wheel.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_wheel.c [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/addconf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/addconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c: In function 'add_conf': /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:331: warning: unused variable 'xpp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dz1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dz0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dy1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dy0' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dx1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:329: warning: unused variable 'dx0'/builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:328: warning: unused variable 'maxincell' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:328: warning: unused variable 'ncells' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:328: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:327: warning: unused variable 'iprot' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:327: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:327: warning: unused variable 'jj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:325: warning: unused variable 'ib2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:325: warning: unused variable 'ib1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/addconf.c:70: warning: 'set_margin' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/calcpot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/calcpot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c: In function 'c_tabpot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:79: warning: unused variable 'qqO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'rinv2O' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'fsO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'vcO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'tzO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'tyO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:78: warning: unused variable 'txO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fzO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fyO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fxO' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fzJ' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fyJ' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:76: warning: unused variable 'fxJ' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:75: warning: unused variable 'ggid' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:71: warning: unused variable 'FF' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:71: warning: unused variable 'fijC' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:70: warning: unused variable 'two' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c: In function 'init_calcpot': /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:222: warning: unused variable 'xtc_traj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c:222: warning: unused variable 'traj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/calcpot.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/edittop.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_bar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c: In function 'delete_from_block': /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c:103: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c:103: warning: unused variable 'j1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c: In function 'delete_atom': /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c:160: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/edittop.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 87%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_membed.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_membed.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'barres_list_create': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:758: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'sample_coll_create_subsample': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1024: warning: unused variable 'hist_end' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1024: warning: unused variable 'hist_start' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'calc_bar_lowlevel': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1253: warning: unused variable 'sum2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1253: warning: unused variable 'sum1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1250: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1249: warning: unused variable 'DG' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'calc_bar': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1616: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1614: warning: unused variable 'nsample2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:1614: warning: unused variable 'nsample1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'read_bar_xvg': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2041: warning: unused variable 'lambda' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'read_edr_rawdh_block': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2087: warning: unused variable 'allocated' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'read_edr_hist_block': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2238: warning: unused variable 'nbin' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'read_barsim_edr': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2286: warning: unused variable 'end_time' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: In function 'gmx_bar': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2608: warning: unused variable 'dg_tot_min' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2608: warning: unused variable 'dg_tot_max' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2608: warning: unused variable 'sig' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2608: warning: unused variable 'dg' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2596: warning: unused variable 'nbs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2594: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2594: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2574: warning: unused variable 'calc_v' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:2574: warning: unused variable 'calc_s' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_bar.c:258: warning: 'samples_destroy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c: In function 'do_md_membed': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:1016: warning: unused variable 'bIterate' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:1013: warning: unused variable 'bTCR' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:1010: warning: unused variable 'timestep' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:986: warning: unused variable 'ebox' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:986: warning: unused variable 'scale_tot' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:976: warning: unused variable 'bCPT' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c: In function 'mdrunner_membed': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2749: warning: unused variable 'nthreads_requested' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2749: warning: unused variable 'nthreads' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2748: warning: unused variable 'cr_old' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2743: warning: unused variable 'list' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2740: warning: unused variable 'gro' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2739: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2739: warning: unused variable 'm'/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 98 /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2729: warning: unused variable 'tmpr2' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2729: warning: unused variable 'tmpr1' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2723: warning: unused variable 'realtime' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:2723: warning: unused variable 'nodetime' [ 88%] /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c: In function 'gmx_membed': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3691: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3642: warning: unused variable 'fptest' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3641: warning: unused variable 'HaveCheckpoint' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3637: warning: unused variable 'ed' Building C object src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_pme_error.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_pme_error.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3506: warning: unused variable 'bPPPME' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c:3505: warning: unused variable 'bCart' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_membed.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_options.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_options.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_options.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_dos.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_dos.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c: In function 'gmx_dos': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:291: warning: unused variable 'dosabs' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:290: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:290: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:288: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_dos.c:143: warning: 'old_calc_fluidicity' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_hydorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_hydorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_densorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/gmx_densorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c: In function 'calc_tetra_order_interface': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c:280: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c:274: warning: unused variable 'subtitle' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/interf.h:46: warning: 'init_interf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c:64: warning: 'print_types' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_hydorder.c:76: warning: 'check_length' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'density_in_time': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:114: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:114: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'outputfield': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:302: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:311: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'filterdensmap': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:348: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:346: warning: unused variable 'output' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'interfaces_txy': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'spread' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'alpha' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'densr' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:380: warning: unused variable 'densl' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:379: warning: unused variable 'deltandx' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: In function 'gmx_densorder': /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:656: warning: unused variable 'title' /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:259: warning: 'printdensavg' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_densorder.c:322: warning: 'periodic_running_average' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/powerspect.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/powerspect.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/powerspect.c /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/tools/interf.h:46: warning: 'init_interf' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 99 [ 88%] [ 89%] Building C object src/tools/CMakeFiles/gmxana.dir/dens_filter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/dens_filter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c Building C object src/tools/CMakeFiles/gmxana.dir/binsearch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -Dgmxana_EXPORTS -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxana.dir/binsearch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/binsearch.c /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c: In function 'periodic_convolution': /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c:96: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c:96: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/tools/dens_filter.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used Linking C shared library libgmxana_d.so cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana.dir/link.txt --verbose=1 /usr/bin/gcc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libgmxana_d.so.6 -o libgmxana_d.so.6 CMakeFiles/gmxana.dir/autocorr.c.o CMakeFiles/gmxana.dir/expfit.c.o CMakeFiles/gmxana.dir/polynomials.c.o CMakeFiles/gmxana.dir/levenmar.c.o CMakeFiles/gmxana.dir/anadih.c.o CMakeFiles/gmxana.dir/pp2shift.c.o CMakeFiles/gmxana.dir/dlist.c.o CMakeFiles/gmxana.dir/eigio.c.o CMakeFiles/gmxana.dir/cmat.c.o CMakeFiles/gmxana.dir/eigensolver.c.o CMakeFiles/gmxana.dir/nsc.c.o CMakeFiles/gmxana.dir/hxprops.c.o CMakeFiles/gmxana.dir/fitahx.c.o CMakeFiles/gmxana.dir/geminate.c.o CMakeFiles/gmxana.dir/gmx_analyze.c.o CMakeFiles/gmxana.dir/gmx_anaeig.c.o CMakeFiles/gmxana.dir/gmx_angle.c.o CMakeFiles/gmxana.dir/gmx_bond.c.o CMakeFiles/gmxana.dir/gmx_bundle.c.o CMakeFiles/gmxana.dir/gmx_chi.c.o CMakeFiles/gmxana.dir/gmx_cluster.c.o CMakeFiles/gmxana.dir/gmx_confrms.c.o CMakeFiles/gmxana.dir/gmx_covar.c.o CMakeFiles/gmxana.dir/gmx_current.c.o CMakeFiles/gmxana.dir/gmx_density.c.o CMakeFiles/gmxana.dir/gmx_densmap.c.o CMakeFiles/gmxana.dir/gmx_dih.c.o CMakeFiles/gmxana.dir/gmx_dielectric.c.o CMakeFiles/gmxana.dir/gmx_kinetics.c.o CMakeFiles/gmxana.dir/gmx_spatial.c.o CMakeFiles/gmxana.dir/gmx_tune_pme.c.o CMakeFiles/gmxana.dir/gmx_dipoles.c.o CMakeFiles/gmxana.dir/gmx_disre.c.o CMakeFiles/gmxana.dir/gmx_dist.c.o CMakeFiles/gmxana.dir/gmx_dyndom.c.o CMakeFiles/gmxana.dir/gmx_enemat.c.o CMakeFiles/gmxana.dir/gmx_energy.c.o CMakeFiles/gmxana.dir/gmx_lie.c.o CMakeFiles/gmxana.dir/gmx_filter.c.o CMakeFiles/gmxana.dir/gmx_gyrate.c.o CMakeFiles/gmxana.dir/gmx_h2order.c.o CMakeFiles/gmxana.dir/gmx_hbond.c.o CMakeFiles/gmxana.dir/gmx_helix.c.o CMakeFiles/gmxana.dir/gmx_mindist.c.o CMakeFiles/gmxana.dir/gmx_msd.c.o CMakeFiles/gmxana.dir/gmx_morph.c.o CMakeFiles/gmxana.dir/gmx_nmeig.c.o CMakeFiles/gmxana.dir/gmx_nmens.c.o CMakeFiles/gmxana.dir/gmx_order.c.o CMakeFiles/gmxana.dir/gmx_principal.c.o CMakeFiles/gmxana.dir/gmx_polystat.c.o 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CMakeFiles/gmxana.dir/gmx_xpm2ps.c.o CMakeFiles/gmxana.dir/gmx_editconf.c.o CMakeFiles/gmxana.dir/gmx_genbox.c.o CMakeFiles/gmxana.dir/gmx_genion.c.o CMakeFiles/gmxana.dir/gmx_genconf.c.o CMakeFiles/gmxana.dir/gmx_genpr.c.o CMakeFiles/gmxana.dir/gmx_eneconv.c.o CMakeFiles/gmxana.dir/gmx_vanhove.c.o CMakeFiles/gmxana.dir/gmx_wheel.c.o CMakeFiles/gmxana.dir/addconf.c.o CMakeFiles/gmxana.dir/calcpot.c.o CMakeFiles/gmxana.dir/edittop.c.o CMakeFiles/gmxana.dir/gmx_bar.c.o CMakeFiles/gmxana.dir/gmx_membed.c.o CMakeFiles/gmxana.dir/gmx_pme_error.c.o CMakeFiles/gmxana.dir/gmx_options.c.o CMakeFiles/gmxana.dir/gmx_dos.c.o CMakeFiles/gmxana.dir/gmx_hydorder.c.o CMakeFiles/gmxana.dir/gmx_densorder.c.o CMakeFiles/gmxana.dir/powerspect.c.o CMakeFiles/gmxana.dir/dens_filter.c.o CMakeFiles/gmxana.dir/binsearch.c.o ../mdlib/libmd_d.so.6 ../gmxlib/libgmx_d.so.6 -lpthread -ldl -lm -lfftw3 -lxml2 cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_symlink_library libgmxana_d.so.6 libgmxana_d.so.6 libgmxana_d.so make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 86 87 88 89 90 91 92 93 94 95 96 97 98 99 [ 89%] Built target gmxana make -f src/tools/CMakeFiles/do_dssp.dir/build.make src/tools/CMakeFiles/do_dssp.dir/depend make -f src/tools/CMakeFiles/editconf.dir/build.make src/tools/CMakeFiles/editconf.dir/depend make -f src/tools/CMakeFiles/eneconv.dir/build.make src/tools/CMakeFiles/eneconv.dir/depend make -f src/tools/CMakeFiles/g_anadock.dir/build.make src/tools/CMakeFiles/g_anadock.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double 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Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/do_dssp.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/do_dssp.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_anadock.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_anadock.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/editconf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/editconf.dir/depend.internal". Scanning dependencies of target eneconv make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/eneconv.dir/build.make src/tools/CMakeFiles/eneconv.dir/build Scanning dependencies of target editconf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/editconf.dir/build.make src/tools/CMakeFiles/editconf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Scanning dependencies of target do_dssp Scanning dependencies of target g_anadock make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/do_dssp.dir/build.make src/tools/CMakeFiles/do_dssp.dir/build [ 89%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' [ 89%] make -f src/tools/CMakeFiles/g_anadock.dir/build.make src/tools/CMakeFiles/g_anadock.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/editconf.dir/editconf.c.o Building C object src/tools/CMakeFiles/eneconv.dir/eneconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o 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-I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_anadock.dir/g_anadock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_anadock.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/do_dssp.dir/do_dssp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/do_dssp.c Linking C executable eneconv_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/eneconv.dir/link.txt --verbose=1 Linking C executable editconf_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/editconf.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/editconf.dir/editconf.c.o -o editconf_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/eneconv.dir/eneconv.c.o -o eneconv_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 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/builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_anaeig.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_anaeig.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_analyze.dir/DependInfo.cmake --color= Scanning dependencies of target g_anaeig make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_anaeig.dir/build.make src/tools/CMakeFiles/g_anaeig.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 89%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_analyze.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_analyze.dir/depend.internal". Scanning dependencies of target g_analyze make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_analyze.dir/build.make src/tools/CMakeFiles/g_analyze.dir/build Building C object src/tools/CMakeFiles/g_anaeig.dir/g_anaeig.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_anaeig.dir/g_anaeig.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_anaeig.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 89%] Building C object src/tools/CMakeFiles/g_analyze.dir/g_analyze.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_analyze.dir/g_analyze.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_analyze.c Linking C executable g_anaeig_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_anaeig.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_anaeig.dir/g_anaeig.c.o -o g_anaeig_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_analyze_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_analyze.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_analyze.dir/g_analyze.c.o -o g_analyze_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 89%] Built target g_anaeig make -f src/tools/CMakeFiles/g_angle.dir/build.make src/tools/CMakeFiles/g_angle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_angle.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_angle.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_angle.dir/depend.internal". Scanning dependencies of target g_angle make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_angle.dir/build.make src/tools/CMakeFiles/g_angle.dir/build [ 89%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 76 Built target g_analyze make -f src/tools/CMakeFiles/g_bar.dir/build.make src/tools/CMakeFiles/g_bar.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bar.dir/DependInfo.cmake --color= [ 90%] Building C object src/tools/CMakeFiles/g_angle.dir/g_angle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_angle.dir/g_angle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_angle.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bar.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bar.dir/depend.internal". Scanning dependencies of target g_bar make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_bar.dir/build.make src/tools/CMakeFiles/g_bar.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Linking C executable g_angle_d Building C object src/tools/CMakeFiles/g_bar.dir/g_bar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_bar.dir/g_bar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_bar.c cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_angle.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_angle.dir/g_angle.c.o -o g_angle_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_bar_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_bar.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_bar.dir/g_bar.c.o -o g_bar_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 76 [ 90%] Built target g_angle make -f src/tools/CMakeFiles/g_bond.dir/build.make src/tools/CMakeFiles/g_bond.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bond.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bond.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bond.dir/depend.internal". [ 90%] Scanning dependencies of target g_bond make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_bond.dir/build.make src/tools/CMakeFiles/g_bond.dir/build Built target g_bar make -f src/tools/CMakeFiles/g_bundle.dir/build.make src/tools/CMakeFiles/g_bundle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bundle.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_bond.dir/g_bond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_bond.dir/g_bond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_bond.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bundle.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bundle.dir/depend.internal". Scanning dependencies of target g_bundle make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_bundle.dir/build.make src/tools/CMakeFiles/g_bundle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Linking C executable g_bond_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_bond.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_bundle.dir/g_bundle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_bundle.dir/g_bundle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_bundle.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_bond.dir/g_bond.c.o -o g_bond_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_bundle_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_bundle.dir/link.txt --verbose=1 Linking C executable g_anadock_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_anadock.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_bundle.dir/g_bundle.c.o -o g_bundle_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_anadock.dir/g_anadock.c.o -o g_anadock_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Built target g_bond make -f src/tools/CMakeFiles/g_chi.dir/build.make src/tools/CMakeFiles/g_chi.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_chi.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_chi.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_chi.dir/depend.internal". [ 90%] Built target g_anadock make -f src/tools/CMakeFiles/g_cluster.dir/build.make src/tools/CMakeFiles/g_cluster.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_cluster.dir/DependInfo.cmake --color= Scanning dependencies of target g_chi make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_chi.dir/build.make src/tools/CMakeFiles/g_chi.dir/build Built target g_bundle make -f src/tools/CMakeFiles/g_clustsize.dir/build.make src/tools/CMakeFiles/g_clustsize.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_cluster.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_cluster.dir/depend.internal". [ 90%] Scanning dependencies of target g_cluster make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_clustsize.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_cluster.dir/build.make src/tools/CMakeFiles/g_cluster.dir/build Building C object src/tools/CMakeFiles/g_chi.dir/g_chi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_chi.dir/g_chi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_chi.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_clustsize.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_clustsize.dir/depend.internal". 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-lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Built target g_cluster make -f src/tools/CMakeFiles/g_confrms.dir/build.make src/tools/CMakeFiles/g_confrms.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_confrms.dir/DependInfo.cmake --color= [ 90%] [ 90%] Built target g_clustsize Built target g_chi make -f src/tools/CMakeFiles/g_covar.dir/build.make src/tools/CMakeFiles/g_covar.dir/depend make -f src/tools/CMakeFiles/g_current.dir/build.make src/tools/CMakeFiles/g_current.dir/depend Linking C executable do_dssp_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/do_dssp.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_covar.dir/DependInfo.cmake --color= make[2]: Entering directory 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[ 91%] Scanning dependencies of target g_covar make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_covar.dir/build.make src/tools/CMakeFiles/g_covar.dir/build Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_current.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_current.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Scanning dependencies of target g_current make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_current.dir/build.make src/tools/CMakeFiles/g_current.dir/build Building C object src/tools/CMakeFiles/g_confrms.dir/g_confrms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_confrms.dir/g_confrms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_confrms.c [ 91%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_covar.dir/g_covar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_covar.dir/g_covar.c.o -c 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CMakeFiles/g_confrms.dir/g_confrms.c.o -o g_confrms_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_covar.dir/link.txt --verbose=1 Linking C executable g_current_d /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_covar.dir/g_covar.c.o -o g_covar_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_current.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_current.dir/g_current.c.o -o g_current_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target do_dssp make -f src/tools/CMakeFiles/g_density.dir/build.make src/tools/CMakeFiles/g_density.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_density.dir/DependInfo.cmake --color= Dependee 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-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_density.dir/g_density.c.o -o g_density_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dielectric.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_densmap.dir/g_densmap.c.o cd 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Scanning dependencies of target g_dielectric Building C object src/tools/CMakeFiles/g_densorder.dir/g_densorder.c.o make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dielectric.dir/build.make src/tools/CMakeFiles/g_dielectric.dir/build cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_densorder.dir/g_densorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_densorder.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Building C object src/tools/CMakeFiles/g_dielectric.dir/g_dielectric.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dielectric.dir/g_dielectric.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dielectric.c Linking C executable g_densmap_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_densmap.dir/link.txt --verbose=1 Linking C executable g_densorder_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_densorder.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_densmap.dir/g_densmap.c.o -o g_densmap_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_densorder.dir/g_densorder.c.o -o g_densorder_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_dielectric_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dielectric.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dielectric.dir/g_dielectric.c.o -o g_dielectric_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_density make -f src/tools/CMakeFiles/g_dih.dir/build.make src/tools/CMakeFiles/g_dih.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dih.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dih.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dih.dir/depend.internal". Scanning dependencies of target g_dih make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dih.dir/build.make src/tools/CMakeFiles/g_dih.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Building C object src/tools/CMakeFiles/g_dih.dir/g_dih.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dih.dir/g_dih.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dih.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_densmap make -f src/tools/CMakeFiles/g_dipoles.dir/build.make src/tools/CMakeFiles/g_dipoles.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dipoles.dir/DependInfo.cmake --color= [ 91%] Built target g_densorder make -f src/tools/CMakeFiles/g_disre.dir/build.make src/tools/CMakeFiles/g_disre.dir/depend Linking C executable g_dih_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dih.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_disre.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dipoles.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dipoles.dir/depend.internal". Scanning dependencies of target g_dipoles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dipoles.dir/build.make src/tools/CMakeFiles/g_dipoles.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 78 Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_disre.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_disre.dir/depend.internal". Scanning dependencies of target g_disre make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_disre.dir/build.make src/tools/CMakeFiles/g_disre.dir/build [ 91%] Built target g_dielectric make -f src/tools/CMakeFiles/g_dist.dir/build.make src/tools/CMakeFiles/g_dist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' [ 92%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dih.dir/g_dih.c.o -o g_dih_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dist.dir/DependInfo.cmake --color= [ 92%] Building C object src/tools/CMakeFiles/g_dipoles.dir/g_dipoles.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dipoles.dir/g_dipoles.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dipoles.c Building C object src/tools/CMakeFiles/g_disre.dir/g_disre.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_disre.dir/g_disre.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_disre.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dist.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dist.dir/depend.internal". Scanning dependencies of target g_dist make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dist.dir/build.make src/tools/CMakeFiles/g_dist.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Linking C executable g_dipoles_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dipoles.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_dist.dir/g_dist.c.o /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dipoles.dir/g_dipoles.c.o -o g_dipoles_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dist.dir/g_dist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dist.c Linking C executable g_disre_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_disre.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_disre.dir/g_disre.c.o -o g_disre_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_dist_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dist.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dist.dir/g_dist.c.o -o g_dist_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Built target g_dih make -f src/tools/CMakeFiles/g_dos.dir/build.make src/tools/CMakeFiles/g_dos.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dos.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dos.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dos.dir/depend.internal". Scanning dependencies of target g_dos make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dos.dir/build.make src/tools/CMakeFiles/g_dos.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 78 [ 92%] [ 92%] Built target g_dipoles make -f src/tools/CMakeFiles/g_dyndom.dir/build.make src/tools/CMakeFiles/g_dyndom.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dyndom.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_dos.dir/g_dos.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dos.dir/g_dos.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dos.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dyndom.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dyndom.dir/depend.internal". [ 92%] Scanning dependencies of target g_dyndom make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dyndom.dir/build.make src/tools/CMakeFiles/g_dyndom.dir/build Built target g_disre make -f src/tools/CMakeFiles/g_enemat.dir/build.make src/tools/CMakeFiles/g_enemat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_enemat.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Linking C executable g_dos_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dos.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_enemat.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_enemat.dir/depend.internal". Building C object src/tools/CMakeFiles/g_dyndom.dir/g_dyndom.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_dyndom.dir/g_dyndom.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_dyndom.c Scanning dependencies of target g_enemat make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_enemat.dir/build.make src/tools/CMakeFiles/g_enemat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dos.dir/g_dos.c.o -o g_dos_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 92%] Building C object src/tools/CMakeFiles/g_enemat.dir/g_enemat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_enemat.dir/g_enemat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_enemat.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable g_dyndom_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_dyndom.dir/link.txt --verbose=1 [ 92%] Built target g_dist make -f src/tools/CMakeFiles/g_energy.dir/build.make src/tools/CMakeFiles/g_energy.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_energy.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_dyndom.dir/g_dyndom.c.o -o g_dyndom_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_enemat_d Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_energy.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_energy.dir/depend.internal". cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_enemat.dir/link.txt --verbose=1 Scanning dependencies of target g_energy make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_energy.dir/build.make src/tools/CMakeFiles/g_energy.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_enemat.dir/g_enemat.c.o -o g_enemat_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 92%] Building C object src/tools/CMakeFiles/g_energy.dir/g_energy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_energy.dir/g_energy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_energy.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Built target g_dos make -f src/tools/CMakeFiles/g_filter.dir/build.make src/tools/CMakeFiles/g_filter.dir/depend Linking C executable g_energy_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_energy.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_filter.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_energy.dir/g_energy.c.o -o g_energy_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Dependee 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Scanning dependencies of target g_filter make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_filter.dir/build.make src/tools/CMakeFiles/g_filter.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 79 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] [ 93%] Built target g_dyndom make -f src/tools/CMakeFiles/g_gyrate.dir/build.make src/tools/CMakeFiles/g_gyrate.dir/depend Building C object src/tools/CMakeFiles/g_filter.dir/g_filter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_filter.dir/g_filter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_filter.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_gyrate.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_gyrate.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_gyrate.dir/depend.internal". Scanning dependencies of target g_gyrate make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_gyrate.dir/build.make src/tools/CMakeFiles/g_gyrate.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable g_filter_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_filter.dir/link.txt --verbose=1 [ 93%] [ 93%] Built target g_enemat make -f src/tools/CMakeFiles/g_h2order.dir/build.make src/tools/CMakeFiles/g_h2order.dir/depend /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_filter.dir/g_filter.c.o -o g_filter_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_gyrate.dir/g_gyrate.c.o make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_h2order.dir/DependInfo.cmake --color= cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_gyrate.dir/g_gyrate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_gyrate.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_h2order.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_h2order.dir/depend.internal". make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Scanning dependencies of target g_h2order make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_h2order.dir/build.make src/tools/CMakeFiles/g_h2order.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' [ 93%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Built target g_energy make -f src/tools/CMakeFiles/g_hbond.dir/build.make src/tools/CMakeFiles/g_hbond.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_hbond.dir/DependInfo.cmake --color= [ 93%] Linking C executable g_gyrate_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_gyrate.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_h2order.dir/g_h2order.c.o Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_hbond.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_hbond.dir/depend.internal". cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_h2order.dir/g_h2order.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_h2order.c Scanning dependencies of target g_hbond /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_gyrate.dir/g_gyrate.c.o -o g_gyrate_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_hbond.dir/build.make src/tools/CMakeFiles/g_hbond.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Building C object src/tools/CMakeFiles/g_hbond.dir/g_hbond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_hbond.dir/g_hbond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_hbond.c Linking C executable g_h2order_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_h2order.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 79 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_h2order.dir/g_h2order.c.o -o g_h2order_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_hbond_d [ 93%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_hbond.dir/link.txt --verbose=1 Built target g_filter make -f src/tools/CMakeFiles/g_helix.dir/build.make src/tools/CMakeFiles/g_helix.dir/depend /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_hbond.dir/g_hbond.c.o -o g_hbond_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_helix.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_helix.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_helix.dir/depend.internal". Scanning dependencies of target g_helix make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_helix.dir/build.make src/tools/CMakeFiles/g_helix.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_helix.dir/g_helix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_helix.dir/g_helix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_helix.c [ 93%] Built target g_gyrate make -f src/tools/CMakeFiles/g_helixorient.dir/build.make src/tools/CMakeFiles/g_helixorient.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_helixorient.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_helixorient.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_helixorient.dir/depend.internal". Scanning dependencies of target g_helixorient make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' Linking C executable g_helix_d make -f src/tools/CMakeFiles/g_helixorient.dir/build.make src/tools/CMakeFiles/g_helixorient.dir/build cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_helix.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_helix.dir/g_helix.c.o -o g_helix_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] [ 93%] Built target g_hbond make -f src/tools/CMakeFiles/g_hydorder.dir/build.make src/tools/CMakeFiles/g_hydorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_hydorder.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_helixorient.dir/g_helixorient.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_helixorient.dir/g_helixorient.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_helixorient.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_hydorder.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_hydorder.dir/depend.internal". /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Scanning dependencies of target g_hydorder make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_hydorder.dir/build.make src/tools/CMakeFiles/g_hydorder.dir/build [ 93%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Built target g_h2order make -f src/tools/CMakeFiles/g_kinetics.dir/build.make src/tools/CMakeFiles/g_kinetics.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_kinetics.dir/DependInfo.cmake --color= [ 93%] Linking C executable g_helixorient_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_helixorient.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_hydorder.dir/g_hydorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_hydorder.dir/g_hydorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_hydorder.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_kinetics.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_kinetics.dir/depend.internal". /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_helixorient.dir/g_helixorient.c.o -o g_helixorient_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Scanning dependencies of target g_kinetics make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_kinetics.dir/build.make src/tools/CMakeFiles/g_kinetics.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Building C object src/tools/CMakeFiles/g_kinetics.dir/g_kinetics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_kinetics.dir/g_kinetics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_kinetics.c Linking C executable g_hydorder_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_hydorder.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_hydorder.dir/g_hydorder.c.o -o g_hydorder_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_kinetics_d [ 93%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_kinetics.dir/link.txt --verbose=1 Built target g_helix make -f src/tools/CMakeFiles/g_lie.dir/build.make src/tools/CMakeFiles/g_lie.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 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Scanning dependencies of target g_lie make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_lie.dir/build.make src/tools/CMakeFiles/g_lie.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 80 [ 94%] Building C object src/tools/CMakeFiles/g_lie.dir/g_lie.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_lie.dir/g_lie.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_lie.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] Built target g_helixorient make -f src/tools/CMakeFiles/g_mdmat.dir/build.make src/tools/CMakeFiles/g_mdmat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_mdmat.dir/DependInfo.cmake --color= Linking C executable g_lie_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_lie.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_mdmat.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_mdmat.dir/depend.internal". Scanning dependencies of target g_mdmat make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_mdmat.dir/build.make src/tools/CMakeFiles/g_mdmat.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_lie.dir/g_lie.c.o -o g_lie_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Built target g_hydorder make -f src/tools/CMakeFiles/g_membed.dir/build.make src/tools/CMakeFiles/g_membed.dir/depend [ 94%] [ 94%] Built target g_kinetics make -f src/tools/CMakeFiles/g_mindist.dir/build.make src/tools/CMakeFiles/g_mindist.dir/depend Building C object src/tools/CMakeFiles/g_mdmat.dir/g_mdmat.c.o make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_membed.dir/DependInfo.cmake --color= cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_mdmat.dir/g_mdmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_mdmat.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_membed.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_membed.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_mindist.dir/DependInfo.cmake --color= Scanning dependencies of target g_membed make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_membed.dir/build.make src/tools/CMakeFiles/g_membed.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable g_mdmat_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_mdmat.dir/link.txt --verbose=1 [ 94%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_mindist.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_mindist.dir/depend.internal". Scanning dependencies of target g_mindist make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_mindist.dir/build.make src/tools/CMakeFiles/g_mindist.dir/build /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_mdmat.dir/g_mdmat.c.o -o g_mdmat_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_membed.dir/g_membed.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_membed.dir/g_membed.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_membed.c [ 94%] Building C object src/tools/CMakeFiles/g_mindist.dir/g_mindist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_mindist.dir/g_mindist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_mindist.c Linking C executable g_membed_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_membed.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 80 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_membed.dir/g_membed.c.o -o g_membed_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_mindist_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_mindist.dir/link.txt --verbose=1 [ 94%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_mindist.dir/g_mindist.c.o -o g_mindist_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Built target g_lie make -f src/tools/CMakeFiles/g_morph.dir/build.make src/tools/CMakeFiles/g_morph.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_morph.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_morph.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_morph.dir/depend.internal". Scanning dependencies of target g_morph make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_morph.dir/build.make src/tools/CMakeFiles/g_morph.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_morph.dir/g_morph.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_morph.dir/g_morph.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_morph.c [ 94%] Built target g_mdmat make -f src/tools/CMakeFiles/g_msd.dir/build.make src/tools/CMakeFiles/g_msd.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_msd.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_msd.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_msd.dir/depend.internal". Built target g_membed make -f src/tools/CMakeFiles/g_nmeig.dir/build.make src/tools/CMakeFiles/g_nmeig.dir/depend Linking C executable g_morph_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_morph.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmeig.dir/DependInfo.cmake --color= Scanning dependencies of target g_msd make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_msd.dir/build.make src/tools/CMakeFiles/g_msd.dir/build [ 94%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Built target g_mindist make -f src/tools/CMakeFiles/g_nmens.dir/build.make src/tools/CMakeFiles/g_nmens.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmens.dir/DependInfo.cmake --color= /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_morph.dir/g_morph.c.o -o g_morph_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 94%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmeig.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmeig.dir/depend.internal". Scanning dependencies of target g_nmeig make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_nmeig.dir/build.make src/tools/CMakeFiles/g_nmeig.dir/build Building C object src/tools/CMakeFiles/g_msd.dir/g_msd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_msd.dir/g_msd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_msd.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmens.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmens.dir/depend.internal". Scanning dependencies of target g_nmens make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_nmens.dir/build.make src/tools/CMakeFiles/g_nmens.dir/build [ 94%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 81 Building C object src/tools/CMakeFiles/g_nmeig.dir/g_nmeig.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_nmeig.dir/g_nmeig.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_nmeig.c Linking C executable g_msd_d [ 95%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_msd.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_nmens.dir/g_nmens.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_nmens.dir/g_nmens.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_nmens.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_msd.dir/g_msd.c.o -o g_msd_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_nmeig_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_nmeig.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_nmeig.dir/g_nmeig.c.o -o g_nmeig_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_nmens_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_nmens.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_nmens.dir/g_nmens.c.o -o g_nmens_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 95%] Built target g_morph make -f src/tools/CMakeFiles/g_nmtraj.dir/build.make src/tools/CMakeFiles/g_nmtraj.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmtraj.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmtraj.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmtraj.dir/depend.internal". Scanning dependencies of target g_nmtraj make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_nmtraj.dir/build.make src/tools/CMakeFiles/g_nmtraj.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_nmtraj.dir/g_nmtraj.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_nmtraj.dir/g_nmtraj.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_nmtraj.c [ 95%] Built target g_msd make -f src/tools/CMakeFiles/g_options.dir/build.make src/tools/CMakeFiles/g_options.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_options.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_nmeig make -f src/tools/CMakeFiles/g_order.dir/build.make src/tools/CMakeFiles/g_order.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_options.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_options.dir/depend.internal". Scanning dependencies of target g_options Linking C executable g_nmtraj_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_nmtraj.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_options.dir/build.make src/tools/CMakeFiles/g_options.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_order.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 81 [ 95%] [ 95%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_nmtraj.dir/g_nmtraj.c.o -o g_nmtraj_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_order.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_order.dir/depend.internal". Built target g_nmens make -f src/tools/CMakeFiles/g_pme_error.dir/build.make src/tools/CMakeFiles/g_pme_error.dir/depend Scanning dependencies of target g_order make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_order.dir/build.make src/tools/CMakeFiles/g_order.dir/build Building C object src/tools/CMakeFiles/g_options.dir/g_options.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_options.dir/g_options.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_options.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_pme_error.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_pme_error.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_pme_error.dir/depend.internal". Scanning dependencies of target g_pme_error make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_pme_error.dir/build.make src/tools/CMakeFiles/g_pme_error.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_order.dir/g_order.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_order.dir/g_order.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_order.c Linking C executable g_options_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_options.dir/link.txt --verbose=1 [ 95%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_options.dir/g_options.c.o -o g_options_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_pme_error.dir/g_pme_error.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_pme_error.dir/g_pme_error.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_pme_error.c Linking C executable g_order_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_order.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_order.dir/g_order.c.o -o g_order_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_pme_error_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_pme_error.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_pme_error.dir/g_pme_error.c.o -o g_pme_error_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 95%] Built target g_nmtraj make -f src/tools/CMakeFiles/g_polystat.dir/build.make src/tools/CMakeFiles/g_polystat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_polystat.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_polystat.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_polystat.dir/depend.internal". make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Scanning dependencies of target g_polystat make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_polystat.dir/build.make src/tools/CMakeFiles/g_polystat.dir/build [ 95%] Built target g_options make -f src/tools/CMakeFiles/g_potential.dir/build.make src/tools/CMakeFiles/g_potential.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double 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Scanning dependencies of target g_potential make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_potential.dir/build.make src/tools/CMakeFiles/g_potential.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_order make -f src/tools/CMakeFiles/g_principal.dir/build.make src/tools/CMakeFiles/g_principal.dir/depend [ 95%] make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_principal.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_potential.dir/g_potential.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_potential.dir/g_potential.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_potential.c Linking C executable g_polystat_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_polystat.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_principal.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_principal.dir/depend.internal". Scanning dependencies of target g_principal make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_principal.dir/build.make src/tools/CMakeFiles/g_principal.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] [ 95%] Built target g_pme_error make -f src/tools/CMakeFiles/g_rama.dir/build.make src/tools/CMakeFiles/g_rama.dir/depend /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_polystat.dir/g_polystat.c.o -o g_polystat_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rama.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_principal.dir/g_principal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_principal.dir/g_principal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_principal.c Linking C executable g_potential_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_potential.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rama.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rama.dir/depend.internal". Scanning dependencies of target g_rama make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rama.dir/build.make src/tools/CMakeFiles/g_rama.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 82 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_potential.dir/g_potential.c.o -o g_potential_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 96%] Linking C executable g_principal_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_principal.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_rama.dir/g_rama.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rama.dir/g_rama.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rama.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_principal.dir/g_principal.c.o -o g_principal_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_rama_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rama.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rama.dir/g_rama.c.o -o g_rama_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_polystat make -f src/tools/CMakeFiles/g_rdf.dir/build.make src/tools/CMakeFiles/g_rdf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rdf.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rdf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rdf.dir/depend.internal". Scanning dependencies of target g_rdf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rdf.dir/build.make src/tools/CMakeFiles/g_rdf.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] [ 96%] Built target g_potential make -f src/tools/CMakeFiles/g_rms.dir/build.make src/tools/CMakeFiles/g_rms.dir/depend Building C object src/tools/CMakeFiles/g_rdf.dir/g_rdf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rdf.dir/g_rdf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rdf.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rms.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_principal make -f src/tools/CMakeFiles/g_rmsdist.dir/build.make src/tools/CMakeFiles/g_rmsdist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rmsdist.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rms.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rms.dir/depend.internal". Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rmsdist.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rmsdist.dir/depend.internal". Scanning dependencies of target g_rms make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rms.dir/build.make src/tools/CMakeFiles/g_rms.dir/build Linking C executable g_rdf_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rdf.dir/link.txt --verbose=1 Scanning dependencies of target g_rmsdist make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rmsdist.dir/build.make src/tools/CMakeFiles/g_rmsdist.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 82 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rdf.dir/g_rdf.c.o -o g_rdf_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 96%] [ 96%] Built target g_rama make -f src/tools/CMakeFiles/g_rmsf.dir/build.make src/tools/CMakeFiles/g_rmsf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rmsf.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_rms.dir/g_rms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rms.dir/g_rms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rms.c Building C object src/tools/CMakeFiles/g_rmsdist.dir/g_rmsdist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rmsdist.dir/g_rmsdist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rmsdist.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rmsf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rmsf.dir/depend.internal". Scanning dependencies of target g_rmsf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rmsf.dir/build.make src/tools/CMakeFiles/g_rmsf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable g_rms_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rms.dir/link.txt --verbose=1 [ 96%] Linking C executable g_rmsdist_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rmsdist.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_rmsf.dir/g_rmsf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rmsf.dir/g_rmsf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rmsf.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rms.dir/g_rms.c.o -o g_rms_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rmsdist.dir/g_rmsdist.c.o -o g_rmsdist_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_rmsf_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rmsf.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rmsf.dir/g_rmsf.c.o -o g_rmsf_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Built target g_rdf make -f src/tools/CMakeFiles/g_rotacf.dir/build.make src/tools/CMakeFiles/g_rotacf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rotacf.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rotacf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rotacf.dir/depend.internal". Scanning dependencies of target g_rotacf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rotacf.dir/build.make src/tools/CMakeFiles/g_rotacf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Building C object src/tools/CMakeFiles/g_rotacf.dir/g_rotacf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rotacf.dir/g_rotacf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rotacf.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_rms make -f src/tools/CMakeFiles/g_rotmat.dir/build.make src/tools/CMakeFiles/g_rotmat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rotmat.dir/DependInfo.cmake --color= [ 96%] Built target g_rmsdist make -f src/tools/CMakeFiles/g_saltbr.dir/build.make src/tools/CMakeFiles/g_saltbr.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rotmat.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rotmat.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_saltbr.dir/DependInfo.cmake --color= Scanning dependencies of target g_rotmat make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rotmat.dir/build.make src/tools/CMakeFiles/g_rotmat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable g_rotacf_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rotacf.dir/link.txt --verbose=1 [ 96%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_saltbr.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_saltbr.dir/depend.internal". make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Scanning dependencies of target g_saltbr make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_saltbr.dir/build.make src/tools/CMakeFiles/g_saltbr.dir/build [ 96%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rotacf.dir/g_rotacf.c.o -o g_rotacf_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_rotmat.dir/g_rotmat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_rotmat.dir/g_rotmat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_rotmat.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 83 Built target g_rmsf make -f src/tools/CMakeFiles/g_sas.dir/build.make src/tools/CMakeFiles/g_sas.dir/depend make[2]: Entering 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Building C object src/tools/CMakeFiles/g_saltbr.dir/g_saltbr.c.o Scanning dependencies of target g_sas cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_saltbr.dir/g_saltbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_saltbr.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sas.dir/build.make src/tools/CMakeFiles/g_sas.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable g_rotmat_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_rotmat.dir/link.txt --verbose=1 [ 97%] Building C object src/tools/CMakeFiles/g_sas.dir/g_sas.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sas.dir/g_sas.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sas.c Linking C executable g_saltbr_d /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_rotmat.dir/g_rotmat.c.o -o g_rotmat_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_saltbr.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_saltbr.dir/g_saltbr.c.o -o g_saltbr_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_sas_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sas.dir/link.txt --verbose=1 make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sas.dir/g_sas.c.o -o g_sas_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 97%] Built target g_rotacf make -f src/tools/CMakeFiles/g_select.dir/build.make src/tools/CMakeFiles/g_select.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_select.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_select.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_select.dir/depend.internal". Scanning dependencies of target g_select make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_select.dir/build.make src/tools/CMakeFiles/g_select.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] [ 97%] Built target g_rotmat make -f src/tools/CMakeFiles/g_sgangle.dir/build.make src/tools/CMakeFiles/g_sgangle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sgangle.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 83 Building C object src/tools/CMakeFiles/g_select.dir/g_select.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_select.dir/g_select.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_select.c [ 97%] Built target g_saltbr make -f src/tools/CMakeFiles/g_sham.dir/build.make src/tools/CMakeFiles/g_sham.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sham.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sgangle.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sgangle.dir/depend.internal". Scanning dependencies of target g_sgangle make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sgangle.dir/build.make src/tools/CMakeFiles/g_sgangle.dir/build /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sham.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sham.dir/depend.internal". Built target g_sas make -f src/tools/CMakeFiles/g_sigeps.dir/build.make src/tools/CMakeFiles/g_sigeps.dir/depend Scanning dependencies of target g_sham [ 97%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sham.dir/build.make src/tools/CMakeFiles/g_sham.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sigeps.dir/DependInfo.cmake --color= Linking C executable g_select_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_select.dir/link.txt --verbose=1 make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_sgangle.dir/g_sgangle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sgangle.dir/g_sgangle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sgangle.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_select.dir/g_select.c.o -o g_select_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 97%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sigeps.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sigeps.dir/depend.internal". Building C object src/tools/CMakeFiles/g_sham.dir/g_sham.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sham.dir/g_sham.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sham.c Linking C executable g_sgangle_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sgangle.dir/link.txt --verbose=1 Scanning dependencies of target g_sigeps make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sigeps.dir/build.make src/tools/CMakeFiles/g_sigeps.dir/build Linking C executable g_sham_d make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sham.dir/link.txt --verbose=1 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sgangle.dir/g_sgangle.c.o -o g_sgangle_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 97%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sham.dir/g_sham.c.o -o g_sham_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_sigeps.dir/g_sigeps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sigeps.dir/g_sigeps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sigeps.c make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] Built target g_select make -f src/tools/CMakeFiles/g_sorient.dir/build.make src/tools/CMakeFiles/g_sorient.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sorient.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sorient.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sorient.dir/depend.internal". Scanning dependencies of target g_sorient make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sorient.dir/build.make src/tools/CMakeFiles/g_sorient.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] [ 97%] [ 97%] Built target g_sgangle Built target g_sham make -f src/tools/CMakeFiles/g_spatial.dir/build.make src/tools/CMakeFiles/g_spatial.dir/depend Building C object src/tools/CMakeFiles/g_sorient.dir/g_sorient.c.o make -f src/tools/CMakeFiles/g_spol.dir/build.make src/tools/CMakeFiles/g_spol.dir/depend cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_sorient.dir/g_sorient.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sorient.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_spatial.dir/DependInfo.cmake --color= make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_spol.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_spatial.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_spatial.dir/depend.internal". Scanning dependencies of target g_spatial Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_spol.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_spol.dir/depend.internal". make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_spatial.dir/build.make src/tools/CMakeFiles/g_spatial.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 84 Scanning dependencies of target g_spol make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_spol.dir/build.make src/tools/CMakeFiles/g_spol.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Linking C executable g_sorient_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sorient.dir/link.txt --verbose=1 [ 98%] Building C object src/tools/CMakeFiles/g_spatial.dir/g_spatial.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_spatial.dir/g_spatial.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_spatial.c /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sorient.dir/g_sorient.c.o -o g_sorient_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_spol.dir/g_spol.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_spol.dir/g_spol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_spol.c Linking C executable g_spatial_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_spatial.dir/link.txt --verbose=1 /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sigeps.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sigeps.c:106: warning: unused variable 'pp' /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_sigeps.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_spatial.dir/g_spatial.c.o -o g_spatial_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Linking C executable g_spol_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_spol.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_spol.dir/g_spol.c.o -o g_spol_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_sorient make -f src/tools/CMakeFiles/g_tcaf.dir/build.make src/tools/CMakeFiles/g_tcaf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_tcaf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 84 [ 98%] Built target g_spatial make -f src/tools/CMakeFiles/g_traj.dir/build.make src/tools/CMakeFiles/g_traj.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_tcaf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_tcaf.dir/depend.internal". cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_traj.dir/DependInfo.cmake --color= Scanning dependencies of target g_tcaf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_tcaf.dir/build.make src/tools/CMakeFiles/g_tcaf.dir/build Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_traj.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_traj.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Scanning dependencies of target g_traj make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_traj.dir/build.make src/tools/CMakeFiles/g_traj.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Building C object src/tools/CMakeFiles/g_tcaf.dir/g_tcaf.c.o [ 98%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_tcaf.dir/g_tcaf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_tcaf.c Built target g_spol make -f src/tools/CMakeFiles/g_tune_pme.dir/build.make src/tools/CMakeFiles/g_tune_pme.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_tune_pme.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/g_traj.dir/g_traj.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_traj.dir/g_traj.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_traj.c Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_tune_pme.dir/DependInfo.cmake" is newer than depender 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Linking C executable g_tcaf_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_tcaf.dir/link.txt --verbose=1 Scanning dependencies of target g_tune_pme make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_tune_pme.dir/build.make src/tools/CMakeFiles/g_tune_pme.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable g_traj_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_traj.dir/link.txt --verbose=1 [ 98%] /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_traj.dir/g_traj.c.o -o g_traj_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_tcaf.dir/g_tcaf.c.o -o g_tcaf_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Building C object src/tools/CMakeFiles/g_tune_pme.dir/g_tune_pme.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_tune_pme.dir/g_tune_pme.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_tune_pme.c Linking C executable g_sigeps_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_sigeps.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_sigeps.dir/g_sigeps.c.o -o g_sigeps_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_tune_pme_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_tune_pme.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_tune_pme.dir/g_tune_pme.c.o -o g_tune_pme_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_traj make -f src/tools/CMakeFiles/g_vanhove.dir/build.make src/tools/CMakeFiles/g_vanhove.dir/depend make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_vanhove.dir/DependInfo.cmake --color= [ 98%] Built target g_tcaf make -f src/tools/CMakeFiles/g_velacc.dir/build.make src/tools/CMakeFiles/g_velacc.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_velacc.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_vanhove.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_vanhove.dir/depend.internal". Scanning dependencies of target g_vanhove make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_vanhove.dir/build.make src/tools/CMakeFiles/g_vanhove.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_velacc.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_velacc.dir/depend.internal". Scanning dependencies of target g_velacc make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_velacc.dir/build.make src/tools/CMakeFiles/g_velacc.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] [ 98%] Built target g_tune_pme make -f src/tools/CMakeFiles/g_wham.dir/build.make src/tools/CMakeFiles/g_wham.dir/depend [ 98%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_wham.dir/DependInfo.cmake --color= /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Building C object src/tools/CMakeFiles/g_vanhove.dir/g_vanhove.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_vanhove.dir/g_vanhove.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_vanhove.c Building C object src/tools/CMakeFiles/g_velacc.dir/g_velacc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_velacc.dir/g_velacc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_velacc.c [ 98%] Built target g_sigeps make -f src/tools/CMakeFiles/g_wheel.dir/build.make src/tools/CMakeFiles/g_wheel.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_wham.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_wham.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_wheel.dir/DependInfo.cmake --color= Scanning dependencies of target g_wham make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_wham.dir/build.make src/tools/CMakeFiles/g_wham.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_wheel.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_wheel.dir/depend.internal". Scanning dependencies of target g_wheel [ 98%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_wheel.dir/build.make src/tools/CMakeFiles/g_wheel.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 85 Linking C executable g_velacc_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_velacc.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/g_wham.dir/g_wham.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o 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-lpthread cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/g_wheel.dir/g_wheel.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/g_wheel.c Linking C executable g_wham_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_wham.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_wham.dir/g_wham.c.o -o g_wham_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable g_wheel_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/g_wheel.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/g_wheel.dir/g_wheel.c.o -o g_wheel_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Built target g_velacc make -f src/tools/CMakeFiles/genbox.dir/build.make src/tools/CMakeFiles/genbox.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd 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Scanning dependencies of target genbox make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/genbox.dir/build.make src/tools/CMakeFiles/genbox.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genconf.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genconf.dir/depend.internal". [ 99%] Scanning dependencies of target genconf make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/genconf.dir/build.make src/tools/CMakeFiles/genconf.dir/build [ 99%] Building C object src/tools/CMakeFiles/genbox.dir/genbox.c.o Built target g_wham cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/genbox.dir/genbox.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/genbox.c make -f src/tools/CMakeFiles/genion.dir/build.make src/tools/CMakeFiles/genion.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genion.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 85 [ 99%] [ 99%] Built target g_wheel make -f src/tools/CMakeFiles/genrestr.dir/build.make src/tools/CMakeFiles/genrestr.dir/depend Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genion.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genion.dir/depend.internal". make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genrestr.dir/DependInfo.cmake --color= Scanning dependencies of target genion make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/genion.dir/build.make src/tools/CMakeFiles/genion.dir/build Building C object src/tools/CMakeFiles/genconf.dir/genconf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/genconf.dir/genconf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/genconf.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Linking C executable genbox_d [ 99%] cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/genbox.dir/link.txt --verbose=1 Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genrestr.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genrestr.dir/depend.internal". Scanning dependencies of target genrestr make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/genrestr.dir/build.make src/tools/CMakeFiles/genrestr.dir/build Building C object src/tools/CMakeFiles/genion.dir/genion.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/genion.dir/genion.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/genion.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/genbox.dir/genbox.c.o -o genbox_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread [ 99%] Linking C executable genconf_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/genconf.dir/link.txt --verbose=1 Building C object src/tools/CMakeFiles/genrestr.dir/genrestr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/genrestr.dir/genrestr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/genrestr.c Linking C executable genion_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/genion.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/genconf.dir/genconf.c.o -o genconf_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/genion.dir/genion.c.o -o genion_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable genrestr_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/genrestr.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/genrestr.dir/genrestr.c.o -o genrestr_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target genbox make -f src/tools/CMakeFiles/make_edi.dir/build.make src/tools/CMakeFiles/make_edi.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/make_edi.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/make_edi.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/make_edi.dir/depend.internal". [ 99%] Built target genconf make -f src/tools/CMakeFiles/make_ndx.dir/build.make src/tools/CMakeFiles/make_ndx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/make_ndx.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/make_ndx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/make_ndx.dir/depend.internal". Built target genrestr make -f src/tools/CMakeFiles/mk_angndx.dir/build.make src/tools/CMakeFiles/mk_angndx.dir/depend Scanning dependencies of target make_edi make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/mk_angndx.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/make_edi.dir/build.make src/tools/CMakeFiles/make_edi.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/mk_angndx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/mk_angndx.dir/depend.internal". [ 99%] [ 99%] Built target genion make -f src/tools/CMakeFiles/trjcat.dir/build.make src/tools/CMakeFiles/trjcat.dir/depend Scanning dependencies of target make_ndx make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/make_ndx.dir/build.make src/tools/CMakeFiles/make_ndx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjcat.dir/DependInfo.cmake --color= Building C object src/tools/CMakeFiles/make_edi.dir/make_edi.c.o make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/make_edi.dir/make_edi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/make_edi.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjcat.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjcat.dir/depend.internal". Scanning dependencies of target trjcat Scanning dependencies of target mk_angndx make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/trjcat.dir/build.make src/tools/CMakeFiles/trjcat.dir/build make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/mk_angndx.dir/build.make src/tools/CMakeFiles/mk_angndx.dir/build Building C object src/tools/CMakeFiles/make_ndx.dir/make_ndx.c.o make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/make_ndx.dir/make_ndx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/make_ndx.c make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] [ 99%] Building C object src/tools/CMakeFiles/trjcat.dir/trjcat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/trjcat.dir/trjcat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/trjcat.c Building C object src/tools/CMakeFiles/mk_angndx.dir/mk_angndx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mk_angndx.dir/mk_angndx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/mk_angndx.c Linking C executable trjcat_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/trjcat.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/trjcat.dir/trjcat.c.o -o trjcat_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used [ 99%] Built target trjcat make -f src/tools/CMakeFiles/trjconv.dir/build.make src/tools/CMakeFiles/trjconv.dir/depend /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjconv.dir/DependInfo.cmake --color= /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/types/../thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not usedDependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjconv.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjconv.dir/depend.internal". /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used Scanning dependencies of target trjconv make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/trjconv.dir/build.make src/tools/CMakeFiles/trjconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 99%] Building C object src/tools/CMakeFiles/trjconv.dir/trjconv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/trjconv.dir/trjconv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/trjconv.c Linking C executable trjconv_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/trjconv.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/trjconv.dir/trjconv.c.o -o trjconv_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target trjconv make -f src/tools/CMakeFiles/trjorder.dir/build.make src/tools/CMakeFiles/trjorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjorder.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjorder.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjorder.dir/depend.internal". Scanning dependencies of target trjorder make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/trjorder.dir/build.make src/tools/CMakeFiles/trjorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Building C object src/tools/CMakeFiles/trjorder.dir/trjorder.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/trjorder.dir/trjorder.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/trjorder.c Linking C executable mk_angndx_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/mk_angndx.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/mk_angndx.dir/mk_angndx.c.o -o mk_angndx_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread Linking C executable trjorder_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/trjorder.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/trjorder.dir/trjorder.c.o -o trjorder_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target mk_angndx make -f src/tools/CMakeFiles/xpm2ps.dir/build.make src/tools/CMakeFiles/xpm2ps.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/xpm2ps.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target trjorder Dependee "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/xpm2ps.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/xpm2ps.dir/depend.internal". Scanning dependencies of target xpm2ps make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/xpm2ps.dir/build.make src/tools/CMakeFiles/xpm2ps.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 100 [100%] Building C object src/tools/CMakeFiles/xpm2ps.dir/xpm2ps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/gcc -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/xpm2ps.dir/xpm2ps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/tools/xpm2ps.c Linking C executable xpm2ps_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/xpm2ps.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/xpm2ps.dir/xpm2ps.c.o -o xpm2ps_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 100 [100%] Built target xpm2ps Linking C executable make_edi_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/make_edi.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/make_edi.dir/make_edi.c.o -o make_edi_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [100%] Built target make_edi Linking C executable make_ndx_d cd /builddir/build/BUILD/gromacs-4.5.5/double/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/make_ndx.dir/link.txt --verbose=1 /usr/bin/gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O3 -DNDEBUG -fPIC CMakeFiles/make_ndx.dir/make_ndx.c.o -o make_ndx_d -rdynamic libgmxana_d.so.6 ../mdlib/libmd_d.so.6 -lfftw3 -lxml2 ../gmxlib/libgmx_d.so.6 -ldl -lm -lpthread make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [100%] Built target make_ndx make[1]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 0 + cd .. + export CC=mpicc + CC=mpicc + export CXX=mpicxx + CXX=mpicxx + export F77=mpif77 + F77=mpif77 + export F90=mpif90 + F90=mpif90 + export FC=mpif90 + FC=mpif90 + . /etc/profile.d/modules.sh ++++ /bin/ps -p 29018 -ocomm= +++ /bin/basename sh ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ MODULESHOME=/usr/share/Modules +++ export MODULESHOME +++ '[' '' = '' ']' +++ LOADEDMODULES= +++ export LOADEDMODULES +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module load openmpi-ppc64 ++ /usr/bin/modulecmd sh load openmpi-ppc64 + eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=openmpi-ppc64' ';export' 'LOADEDMODULES;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-ppc64' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-ppc64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-ppc64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-ppc64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/usr/lib64/python2.6/site-packages/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-ppc64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/bin' ';export' 'PATH;PYTHONPATH=/usr/lib64/python2.6/site-packages/openmpi' ';export' 'PYTHONPATH;_LMFILES_=/etc/modulefiles/openmpi-ppc64' ';export' '_LMFILES_;' ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ LOADEDMODULES=openmpi-ppc64 ++ export LOADEDMODULES ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ MPI_COMPILER=openmpi-ppc64 ++ export MPI_COMPILER ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-ppc64 ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_INCLUDE=/usr/include/openmpi-ppc64 ++ export MPI_INCLUDE ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ MPI_MAN=/usr/share/man/openmpi-ppc64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.6/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-ppc64 ++ export MPI_SYSCONFIG ++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/bin ++ export PATH ++ PYTHONPATH=/usr/lib64/python2.6/site-packages/openmpi ++ export PYTHONPATH ++ _LMFILES_=/etc/modulefiles/openmpi-ppc64 ++ export _LMFILES_ + export 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + SUFFIXCONF='-D GMX_DEFAULT_SUFFIX=OFF -D GMX_BINARY_SUFFIX= -D GMX_LIBS_SUFFIX=_openmpi' + mkdir openmpi-single + cd openmpi-single + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export FFLAGS + /usr/bin/cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DCMAKE_SKIP_RPATH:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=ON -D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=lib64 -D GMX_DOUBLE=OFF -D GMX_MPI=ON -D GMX_DEFAULT_SUFFIX=OFF -D GMX_BINARY_SUFFIX= -D GMX_LIBS_SUFFIX=_openmpi .. -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/lib64/openmpi/bin/mpicc -- Check for working C compiler: /usr/lib64/openmpi/bin/mpicc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/lib64/openmpi/bin/mpicxx -- Check for working CXX compiler: /usr/lib64/openmpi/bin/mpicxx -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Failed -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Failed -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Using manually set binary suffix: "" -- Using manually set library suffix: "_openmpi" WARNING There are known problems with some MPI implementations: OpenMPI version < 1.4.1 MVAPICH2 version <= 1.4.1 * -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Checking for CRAY XT Catamount compile -- Checking for CRAY XT Catamount target - no -- Looking for include files HAVE_STRING_H -- Looking for include files HAVE_STRING_H - found -- Looking for include files HAVE_MATH_H -- Looking for include files HAVE_MATH_H - found -- Looking for include files HAVE_LIMITS_H -- Looking for include files HAVE_LIMITS_H - found -- Looking for include files HAVE_MEMORY_H -- Looking for include files HAVE_MEMORY_H - found -- Looking for include files HAVE_UNISTD_H -- Looking for include files HAVE_UNISTD_H - found -- Looking for include files HAVE_DIRECT_H -- Looking for include files HAVE_DIRECT_H - not found. -- Looking for include files HAVE_PWD_H -- Looking for include files HAVE_PWD_H - found -- Looking for include files HAVE_STDINT_H -- Looking for include files HAVE_STDINT_H - found -- Looking for include files HAVE_STDLIB_H -- Looking for include files HAVE_STDLIB_H - found -- Looking for include files HAVE_PTHREAD_H -- Looking for include files HAVE_PTHREAD_H - found -- Looking for include files HAVE_DIRENT_H -- Looking for include files HAVE_DIRENT_H - found -- Looking for include files HAVE_INTTYPES_H -- Looking for include files HAVE_INTTYPES_H - found -- Looking for include files HAVE_REGEX_H -- Looking for include files HAVE_REGEX_H - found -- Looking for include files HAVE_SYS_TYPES_H -- Looking for include files HAVE_SYS_TYPES_H - found -- Looking for include files HAVE_SYS_STAT_H -- Looking for include files HAVE_SYS_STAT_H - found -- Looking for include files HAVE_SYS_TIME_H -- Looking for include files HAVE_SYS_TIME_H - found -- Looking for include files HAVE_RPC_RPC_H -- Looking for include files HAVE_RPC_RPC_H - found -- Looking for include files HAVE_RPC_XDR_H -- Looking for include files HAVE_RPC_XDR_H - found -- Looking for include files HAVE_XMMINTRIN_H -- Looking for include files HAVE_XMMINTRIN_H - not found. -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - not found. -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include files HAVE_PMMINTRIN_H - not found. -- Looking for include files HAVE_SMMINTRIN_H -- Looking for include files HAVE_SMMINTRIN_H - not found. -- Looking for include files HAVE_IO_H -- Looking for include files HAVE_IO_H - not found. -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strdup -- Looking for strdup - found -- Looking for vprintf -- Looking for vprintf - found -- Looking for memcmp -- Looking for memcmp - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Looking for _aligned_malloc -- Looking for _aligned_malloc - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for isnan -- Looking for isnan - found -- Looking for _isnan -- Looking for _isnan - not found -- Looking for isfinite -- Looking for isfinite - not found -- Looking for _isfinite -- Looking for _isfinite - not found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for cbrt in m -- Looking for cbrt in m - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of bool -- Check size of bool - failed -- Check size of int -- Check size of int - done -- Check size of long int -- Check size of long int - done -- Check size of long long int -- Check size of long long int - done -- Check size of off_t -- Check size of off_t - done -- Check size of void * -- Check size of void * - done -- Check size of uid_t -- Check size of uid_t - done -- Check size of gid_t -- Check size of gid_t - done -- Check size of size_t -- Check size of size_t - done -- Check size of off_t -- Check size of off_t - done -- Check if the system is big endian -- Searching 16 bit integer -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - big endian -- checking for module 'libxml-2.0' -- found libxml-2.0, version 2.7.6 -- Found LibXml2: /usr/lib64/libxml2.so -- Setting build user & time -- Setting build user & time - OK -- Checking floating point format -- Checking floating point format - unknown -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for return type of signals -- Checking for return type of signals - void -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for inline keyword -- Checking for inline keyword - inline -- Checking for inline keyword -- Checking for inline keyword - inline -- Checking for pipe support -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Checking for MSVC x86 inline asm -- Checking for MSVC x86 inline asm - not supported -- Checking for system XDR support -- Checking for system XDR support - present -- Found FFTW3F: /usr/lib64/libfftw3f.so -- Found assembler: /usr/bin/as -- Loaded CMakeASM-ATTInformation - ASM-ATT support is still experimental, please report issues -- Configuring done -- Generating done -- Build files have been written to: /builddir/build/BUILD/gromacs-4.5.5/openmpi-single + make VERBOSE=1 -j4 mdrun /usr/bin/cmake -H/builddir/build/BUILD/gromacs-4.5.5 -B/builddir/build/BUILD/gromacs-4.5.5/openmpi-single --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 mdrun make[1]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -H/builddir/build/BUILD/gromacs-4.5.5 -B/builddir/build/BUILD/gromacs-4.5.5/openmpi-single --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 73 make -f CMakeFiles/Makefile2 src/kernel/CMakeFiles/mdrun.dir/all make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/depend make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/openmpi-single /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib/CMakeFiles/gmx.dir/depend.internal". Scanning dependencies of target gmx make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/build make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 0%] [ 0%] [ 0%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/princ.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/topsort.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_fatal.c.o [ 0%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_fatal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_fatal.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/topsort.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/princ.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c Building C object src/gmxlib/CMakeFiles/gmx.dir/random.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/random.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c: In function 'gmx_sort_ilist_fe': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c:185: warning: unused variable 'bPert' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c: In function 'maxwell_speed': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c:93: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c:92: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_fatal.c:150: warning: 'bputi' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 0%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not usedBuilding C object src/gmxlib/CMakeFiles/gmx.dir/checkpoint.c.o /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/checkpoint.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c:48: warning: 'm_op' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c:249: warning: 'dump_shit' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_real': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:448: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_ints': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:459: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_doubles': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:526: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_rvecs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:591: warning: unused variable 'n3' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpt_header': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:700: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpt_files': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1043: warning: unused variable 'j' [ 0%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'write_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1159: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1154: warning: unused variable 'flag_64bit' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'read_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1459: warning: unused variable 'filename' Building C object src/gmxlib/CMakeFiles/gmx.dir/dihres.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/dihres.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'list_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2001: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2001: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2000: warning: unused variable 'indent' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:429: warning: 'do_cpte_reals' defined but not used [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_cyclecounter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_cyclecounter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_cyclecounter.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 1 [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/warninp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/warninp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/warninp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c: In function 'ta_dihres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c:78: warning: unused variable 'dp2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c:77: warning: unused variable 'typep' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sfactor.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sfactor.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sfactor.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ifunc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ifunc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ifunc.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 1%] [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ffscanf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ffscanf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ffscanf.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_system_xdr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_system_xdr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_system_xdr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/macros.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/macros.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/macros.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 2 [ 1%] [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/shift_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/shift_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c Building C object src/gmxlib/CMakeFiles/gmx.dir/atomprop.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/atomprop.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c: In function 'gmx_atomprop_init': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c:246: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c: In function 'shift_LRcorrection': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:271: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:267: warning: unused variable 'qtot' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:266: warning: unused variable 'isp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:384: warning: 'rgbset' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrnb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrnb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrnb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/tpxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/tpxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_pullgrp': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:212: warning: unused variable 'i' [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/calch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/calch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_iparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:931: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ilist': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1179: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1200: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ilists': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1262: warning: unused variable 'bDum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1261: warning: unused variable 'renum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1261: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_grps': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1382: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1498: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1498: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_atomtypes': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1525: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_moltype': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1678: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_molblock': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1706: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_mtop': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1834: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2046: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'read_tpx_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2347: warning: unused variable 'ltop' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'read_tps_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2376: warning: unused variable 'topconv' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c: In function 'gen_waterhydrogen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c:82: warning: unused variable 'kkk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/wman.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/wman.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/string2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/string2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'mydate': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:202: warning: unused variable 'num' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'print_tty_formatted': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:551: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_wikiman': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:672: warning: unused variable 'tmp2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:671: warning: unused variable 'link' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_htmlman': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:723: warning: unused variable 'link' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_py': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:966: warning: unused variable 'bHidden' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c: In function 'ltrim': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c:137: warning: unused variable 'tr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/matio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/matio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c: In function 'write_xpm_map_split': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'fac' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:661: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 3 [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pargs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pargs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c: In function 'print_pargs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'buf2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_asc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_asc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_asc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 4%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/index.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/index.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c Building C object src/gmxlib/CMakeFiles/gmx.dir/xtcio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xtcio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xtcio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'analyse_prot': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:365: warning: unused variable 'nnpres' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'gmx_residuetype_add': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:514: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'gmx_residuetype_init': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:546: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:545: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'analyse': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:734: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:732: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pdbio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pdbio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/readinp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/readinp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: In function 'gmx_conect_add': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:681: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: In function 'read_pdbfile': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:705: warning: unused variable 'chidmax' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:704: warning: unused variable 'nres_ter_prev' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: In function 'get_einp': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c:283: warning: unused variable 'warn_buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: In function 'get_eenum': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c:456: warning: unused variable 'dum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/main.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/main.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 4 [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/orires.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/orires.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'par_fn': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:140: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'gmx_log_open': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:259: warning: unused variable 'testlen' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'init_multisystem': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:485: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'init_par': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:522: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: At top level:/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/calcgrid.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/calcgrid.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c: In function 'init_orires': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c:58: warning: unused variable 'nr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c: In function 'calc_grid': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c:98: warning: unused variable 'j' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 5%] [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statutil.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/sortwater.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sortwater.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sortwater.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pbc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pbc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'set_default_time_unit': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:255: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'set_default_xvg_format': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:287: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:286: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'parse_common_args': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:578: warning: unused variable 'envstr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:577: warning: unused variable 'newdesc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:577: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:536: warning: unused variable 'npri_pa' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:529: warning: unused variable 'mantp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:409: warning: 'pdesc' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'low_set_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:285: warning: unused variable 'bXY' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'put_atom_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1195: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'put_atoms_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1209: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1209: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trnio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trnio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trnio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_remove': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:339: warning: unused variable 'prev' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_open': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:438: warning: unused variable 'xdrid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:435: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_fopen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:640: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_fclose': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:654: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_int_get_file_position': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:783: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_get_output_file_positions': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:858: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:837: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:835: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:834: warning: unused variable 'pos_lo' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:834: warning: unused variable 'pos_hi' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:833: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:833: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_int_fsync': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:1005: warning: unused variable 'filen' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 5 [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/maths.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/maths.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mtxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: In function 'gmx_mtxio_write': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c:92: warning: unused variable 'bRead' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: In function 'gmx_mtxio_read': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c:166: warning: unused variable 'bRead' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 6%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/xvgr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xvgr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/libxdrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/libxdrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/replace.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/replace.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/replace.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr3dfcoord': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:820: warning: unused variable 'xdrid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'xvgropen_type': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:287: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xtc_get_next_frame_start': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'fgets3': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:442: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1546: warning: unused variable 'inp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr_xtc_seek_time': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1693: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr_xtc_get_last_frame_number': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1882: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'read_xvg_legend': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:546: warning: unused variable 'ptr1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:546: warning: unused variable 'ptr0' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'read_xvg_time': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:697: warning: unused variable 'tend' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/viewit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/viewit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/viewit.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/strdb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/strdb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/strdb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 6 [ 6%] [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/enxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/enxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c Building C object src/gmxlib/CMakeFiles/gmx.dir/splitter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/splitter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/filenm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/filenm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'do_enxnms': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:392: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'do_eheader': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:448: warning: unused variable 'tempfix_nr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:446: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'open_enx': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:723: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_force2': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:116: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'mk_border': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:346: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_blocks': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:424: warning: unused variable 'bSHK' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:420: warning: unused variable 'last_shk'/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'get_enx_state': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:1071: warning: unused variable 'pcouplmu_nm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:419: warning: unused variable 'ai' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:419: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'merge_sid': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:662: warning: unused variable 'nChanged' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'gen_sblocks': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:760: warning: unused variable 'isid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'istart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'find_constraint_range_recursive': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:866: warning: unused variable 'nconstr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'pd_determine_constraints_range': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:890: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:890: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'minidx' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'ihome' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'minhome' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:932: warning: unused variable 'ia' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nrd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nra' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nvsite_constr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'ftype' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'nodeid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'bstart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'send' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'sstart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'maxatom' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'atom' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'mj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:375: warning: 'gen_units' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: In function 'set_default_file_name': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c:216: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:832: warning: 'block2blocka' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: In function 'add_suffix_to_output_names': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c:951: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rmpbc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rmpbc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rmpbc.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/inputrec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/inputrec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/inputrec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rando.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rando.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rando.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/bondfree.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 8%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 7 [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/vmddlopen.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmddlopen.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'FENE_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:242: warning: unused variable 'dr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'do_1_thole': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:652: warning: unused variable 'r12n' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'posres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1254: warning: unused variable 'ki' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'cmap_dihs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1642: warning: unused variable 'psi2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1641: warning: unused variable 'psi1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1637: warning: unused variable 'l4' [ 9%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'bonded_tab': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2350: warning: unused variable 'f' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2350: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'tab_angles': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2475: warning: unused variable 'snt' Building C object src/gmxlib/CMakeFiles/gmx.dir/txtdump.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/txtdump.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c: In function 'choose_ff': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c:441: warning: unused variable 'eFF' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_qm_opts': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:991: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_block_title': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1037: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_blocka_title': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1050: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_block': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1103: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_atom': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1225: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1260: warning: unused variable 'grpnr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_header': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1423: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1063: warning: 'low_pr_block' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/writeps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/writeps.c /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxcpp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxcpp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: In function 'cpp_open_file': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c:188: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: In function 'cpp_close_file': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c:577: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_xdr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_xdr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_xdr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_matrix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_matrix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sighandler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sighandler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sighandler.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: In function 'free_matrix': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c:63: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: In function 'multi_regression': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c:174: warning: unused variable 'niter' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 8 [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_arpack.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_arpack.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_arpack.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/vmdio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c: In function 'load_vmd_library': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c:234: warning: unused variable 'filename' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/names.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/names.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/names.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrjac.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrjac.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrjac.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/confio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/confio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/do_fit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/do_fit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: In function 'read_espresso_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:451: warning: unused variable 'npar' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:451: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: In function 'read_stx_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:1397: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:1392: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:880: warning: 'get_conf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: In function 'calc_fit_R': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c:104: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: In function 'do_fit_ndim': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c:215: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/typedefs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/typedefs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_block': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:108: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_blocka': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:118: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_atom': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:131: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:183: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_state': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:533: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 9 [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/symtab.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/symtab.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/symtab.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mvdata.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mvdata.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_atoms': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:169: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:187: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:327: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:349: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_inputrec': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:466: warning: unused variable 'bAlloc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_molblock': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:497: warning: unused variable 'bAlloc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:312: warning: 'bc_idef' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sparsematrix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sparsematrix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sparsematrix.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gbutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gbutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gbutil.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mshift.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mshift.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/md5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/md5.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: In function 'compact_graph': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c:249: warning: unused variable 'e' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: In function 'done_graph': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c:405: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/futil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/futil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 10 [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/tcontrol.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/tcontrol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tcontrol.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c: In function 'ffopen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c:446: warning: unused variable 'bf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ewald_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ewald_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ewald_util.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/smalloc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/smalloc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c: In function 'save_free_aligned': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c:356: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c:356: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/oenv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/oenv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/oenv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 13%] [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_sort.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_sort.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_sort.c Building C object src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/3dview.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c: In function 'reset_view': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c:281: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mtop_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrama.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrama.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_atomnr_to_molblock_ind': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:150: warning: unused variable 'atoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_atominfo_global': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:177: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_ilistloop_all_next': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:449: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_global_cgs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:503: warning: unused variable 'atoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gen_local_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:773: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:773: warning: unused variable 'ftype_dest' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 11 [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/wgms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/wgms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wgms.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: In function 'get_dih2': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:182: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: In function 'init_rama': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:312: warning: unused variable 'ePBC' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:179: warning: 'get_dih2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rbin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rbin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rbin.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/chargegroup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/chargegroup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/chargegroup.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/network.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/network.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/invblock.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/invblock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/invblock.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: In function 'gmx_setup': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:82: warning: unused variable 'flag' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:82: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:80: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xdrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xdrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xdrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/disre.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/disre.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 12 [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_rw.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_rw.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_rw.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 16%] [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_bin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_bin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_bin.c Building C object src/gmxlib/CMakeFiles/gmx.dir/cinvsqrtdata.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/cinvsqrtdata.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/cinvsqrtdata.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: In function 'calc_disres_R_6': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'jt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'kj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'ki' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: In function 'ta_disres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:372: warning: unused variable 'jt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:372: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/copyrite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/copyrite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 16%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: In function 'cool_quote': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c:193: warning: unused variable 's' Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_random.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: In function 'please_cite':cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_random.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c:535: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selvalue.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selvalue.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selvalue.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_permute.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c: In function 'gmx_rng_update': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c:217: warning: unused variable 'lastx' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 13 [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_same.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: In function 'init_output_permute': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c:192: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: In function 'evaluate_permute': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c:240: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c: In function 'evaluate_same_str': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c:499: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 17%] [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selelem.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selhelp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selhelp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selhelp.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selelem.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selelem.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/scanner.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/scanner.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/scanner.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 17%] scanner.c:1396: warning: 'yyunput' defined but not used scanner.c:1438: warning: 'input' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/parsetree.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/parsetree.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_selelem_set_method': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:556: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_sel_init_comparison': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:652: warning: unused variable 'rc' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_sel_init_modifier': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:835: warning: unused variable 'i' [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_insolidangle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_insolidangle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/scanner_internal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/scanner_internal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/scanner_internal.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: In function 'evaluate_insolidangle': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:476: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: In function 'store_surface_point': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:829: warning: unused variable 'bin' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:829: warning: unused variable 'pbin' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:213: warning: 'set_comg_insolidangle' declared 'static' but never defined /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 14 [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/symrec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 19%] [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/parser.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/compiler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/compiler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/parser.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parser.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c: In function 'add_symbol': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c:395: warning: unused variable 'len' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_distance.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_distance.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_distance.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c: In function 'analyze_static': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c:2004: warning: unused variable 'next' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c:2004: warning: unused variable 'child' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/mempool.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/mempool.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/mempool.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/params.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/params.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_compare.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_compare.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_compare.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c: In function 'parse_values_varnum_expr': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c:676: warning: unused variable 'expr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 15 [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_position.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_position.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_keywords.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_keywords.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_keywords.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selection.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selection.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selection.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_simple.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_simple.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selmethod.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selmethod.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selmethod.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/evaluate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/evaluate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/evaluate.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_merge.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_merge.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/trajana.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c: In function 'init_merge': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c:182: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 16 [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/position.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/position.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: In function 'gmx_ana_traj_free': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c:322: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: In function 'gmx_ana_init_selections': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c:1200: warning: unused variable 'bOk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/poscalc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: In function 'merge_to_base': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c:797: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: In function 'gmx_ana_poscalc_update': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c:1282: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/nbsearch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/nbsearch.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/displacement.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/displacement.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/indexutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/indexutil.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/centerofmass.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c: In function 'gmx_calc_cog': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c:55: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: In function 'gmx_stats_dump_xy': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c:449: warning: unused variable 'ok' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: In function 'gmx_stats_make_histogram': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c:505: warning: unused variable 'ok' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 17 [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statistics/histogram.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/histogram.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_generic_cg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_generic_cg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c: In function 'gmx_nb_generic_cg_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:83: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:62: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:61: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nonbonded.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nonbonded.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 23%] [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_free_energy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_free_energy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_generic.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_generic.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: In function 'do_nonbonded': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:313: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:311: warning: unused variable 'bWater' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:309: warning: unused variable 'sz' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: In function 'do_listed_vdw_q': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:664: warning: unused variable 'tmplist' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:655: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel230.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel230.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c: In function 'gmx_nb_free_energy_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:102: warning: unused variable 'H' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:102: warning: unused variable 'G' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:91: warning: unused variable 'rinvsix' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:88: warning: unused variable 'vcoul' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c: In function 'gmx_nb_generic_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:81: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:61: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:60: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: In function 'nb_kernel230': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: In function 'nb_kernel230nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c:336: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel213.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel213.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 18 [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel312.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel312.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel101.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel101.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel223.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel223.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: In function 'nb_kernel213': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: In function 'nb_kernel213nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c:424: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: In function 'nb_kernel312': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: In function 'nb_kernel312nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c:733: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: At top level:/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: In function 'nb_kernel101': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: In function 'nb_kernel101nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c:368: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: In function 'nb_kernel223': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: In function 'nb_kernel223nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c:427: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 24%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel334.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel334.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel210.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel210.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: In function 'nb_kernel334': [ 24%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: In function 'nb_kernel334nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c:798: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel112.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel112.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: In function 'nb_kernel210': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: In function 'nb_kernel210nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c:304: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: In function 'nb_kernel112': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: In function 'nb_kernel112nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c:574: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In function 'nb_kernel200': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In function 'nb_kernel200nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:286: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 19 [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel130.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel130.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel211.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel211.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: In function 'nb_kernel130': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: In function 'nb_kernel130nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c:334: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel214.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel214.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: In function 'nb_kernel211': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: In function 'nb_kernel211nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c:390: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: In function 'nb_kernel214': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: In function 'nb_kernel214nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c:622: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel110.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel110.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel131.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel131.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c: In function 'setup_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c:113: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: In function 'nb_kernel110': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: In function 'nb_kernel110nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c:302: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: In function 'nb_kernel131': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: In function 'nb_kernel131nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c:418: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel232.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel232.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 20 [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel303.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel303.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: In function 'nb_kernel232': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: In function 'nb_kernel232nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c:616: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel304.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel304.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel124.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel124.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: In function 'nb_kernel303': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: In function 'nb_kernel303nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: In function 'nb_kernel304': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: In function 'nb_kernel304nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c:715: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: In function 'nb_kernel124': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: In function 'nb_kernel124nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c:615: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel430.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel430.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c: In function 'nb_kernel430': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c:105: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel221.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel221.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 27%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: In function 'nb_kernel221': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: In function 'nb_kernel221nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c:392: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel420.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel420.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel400.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel400.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel100.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel100.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c: In function 'nb_kernel420': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c:105: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c: In function 'nb_kernel400': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c:100: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: In function 'nb_kernel100': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: In function 'nb_kernel100nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c:284: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 21 [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel030.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel030.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel132.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel132.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 28%] [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel302.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel302.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel233.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel233.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: In function 'nb_kernel030': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: In function 'nb_kernel030nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c:322: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: In function 'nb_kernel132': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: In function 'nb_kernel132nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c:606: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: In function 'nb_kernel302': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: In function 'nb_kernel302nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c:715: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: In function 'nb_kernel233': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: In function 'nb_kernel233nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c:456: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel320.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel320.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: In function 'nb_kernel320': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: In function 'nb_kernel320nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c:327: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel123.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel123.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 28%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 22 [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel204.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel204.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: In function 'nb_kernel123': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: In function 'nb_kernel123nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: In function 'nb_kernel204': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: In function 'nb_kernel204nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c:568: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c: In function 'setup_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c:114: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel313.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel313.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: In function 'nb_kernel313': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: In function 'nb_kernel313nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c:476: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel314.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel314.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel333.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel333.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: In function 'nb_kernel314': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: In function 'nb_kernel314nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c:770: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: In function 'nb_kernel333': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: In function 'nb_kernel333nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c:504: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used[ 30%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel311.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel311.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: In function 'nb_kernel311': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: In function 'nb_kernel311nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c:443: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel331.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel331.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: In function 'nb_kernel331': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: In function 'nb_kernel331nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c:460: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel113.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel113.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 23 [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel121.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel121.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: In function 'nb_kernel113': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: In function 'nb_kernel113nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c:420: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: In function 'nb_kernel121': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: In function 'nb_kernel121nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c:388: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel010.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel010.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: In function 'nb_kernel010': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c:85: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: In function 'nb_kernel010nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c:292: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 31%] [ 31%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel330.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel201.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel201.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel330.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel102.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel102.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel020.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel020.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: In function 'nb_kernel330': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: In function 'nb_kernel330nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c:342: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: In function 'nb_kernel102': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: In function 'nb_kernel102nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c:558: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: In function 'nb_kernel201': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: In function 'nb_kernel201nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c:372: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: In function 'nb_kernel020': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: In function 'nb_kernel020nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c:294: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel231.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel231.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 24 [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel203.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel203.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel133.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel133.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: In function 'nb_kernel231': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: In function 'nb_kernel231nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c:422: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: In function 'nb_kernel203': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: In function 'nb_kernel203nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c:372: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel224.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel224.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: In function 'nb_kernel133': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: In function 'nb_kernel133nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c:452: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: In function 'nb_kernel224': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: In function 'nb_kernel224nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c:625: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel323.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel323.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel103.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel103.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: In function 'nb_kernel323': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: In function 'nb_kernel323nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c:479: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: In function 'nb_kernel103': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: In function 'nb_kernel103nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c:368: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel322.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel322.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 32%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 25 Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel104.c.o [ 34%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel104.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel324.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel324.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: In function 'nb_kernel322': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: In function 'nb_kernel322nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c:735: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel410.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel410.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: In function 'nb_kernel104': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: In function 'nb_kernel104nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c:558: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: In function 'nb_kernel324': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: In function 'nb_kernel324nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c:773: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c: In function 'nb_kernel410': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c:106: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel202.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel202.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 34%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: In function 'nb_kernel202': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: In function 'nb_kernel202nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c:568: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel212.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel212.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: In function 'nb_kernel212': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: In function 'nb_kernel212nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c:584: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel114.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel114.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel222.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel222.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: In function 'nb_kernel114': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: In function 'nb_kernel114nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c:612: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel332.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel332.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: In function 'nb_kernel222': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: In function 'nb_kernel222nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c:586: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: In function 'nb_kernel332': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: In function 'nb_kernel332nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c:750: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel300.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel300.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: In function 'nb_kernel300': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: In function 'nb_kernel300nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c:305: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 26 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 35%] [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_c.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_c.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel301.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel301.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel134.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel134.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: In function 'nb_kernel301': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c:84: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: In function 'nb_kernel301nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: At top level:[ 35%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel321.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel321.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: In function 'nb_kernel134': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: In function 'nb_kernel134nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c:644: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: In function 'nb_kernel321': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: In function 'nb_kernel321nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c:445: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel234.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel234.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel310.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel310.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: In function 'nb_kernel234': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: In function 'nb_kernel234nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c:654: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel122.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel122.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: In function 'nb_kernel310': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: In function 'nb_kernel310nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c:325: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 27 [ 36%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: In function 'nb_kernel122': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c:84: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel111.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: In function 'nb_kernel122nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c:576: warning: unused variable 'gbtabscale' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel111.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel120.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel120.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: In function 'nb_kernel111': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: In function 'nb_kernel111nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c:386: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: In function 'nb_kernel120': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: In function 'nb_kernel120nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c:304: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 36%] [ 36%] [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sger.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sger.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sger.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel220.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel220.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/srot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/srot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/srot.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 36%] [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dswap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dswap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dswap.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sgemm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sgemm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sgemm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 28 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: In function 'nb_kernel220': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: In function 'nb_kernel220nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c:306: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 38%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dasum.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dasum.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dasum.c [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/daxpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/daxpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/daxpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 38%] [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/idamax.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/idamax.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/idamax.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dger.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dger.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dger.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dscal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dscal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dscal.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 38%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strmm.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrsm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrsm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrsm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 29 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 39%] [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ssyr2.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ddot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ddot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ddot.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ssyr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssyr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sscal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sscal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sscal.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 39%] [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/isamax.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/isamax.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/isamax.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsyr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsyr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsyr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dgemv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dgemv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dgemv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsyr2k.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 30 cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsyr2k.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsyr2k.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 41%] [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dgemm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dgemm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dgemm.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrmv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrmv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrmv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dcopy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dcopy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dcopy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 41%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sasum.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sasum.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sasum.c [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sgemv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sgemv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sgemv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsymv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsymv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsymv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/scopy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/scopy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/scopy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 31 [ 42%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/saxpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/saxpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/saxpy.c [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sswap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sswap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sswap.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/drot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/drot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/drot.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 42%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 42%] [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sdot.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sdot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sdot.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dnrm2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dnrm2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dnrm2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ssymv.c.o [ 42%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ssymv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssymv.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ssyr2k.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ssyr2k.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssyr2k.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 32 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 43%] [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strmv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strmv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strmv.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/snrm2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/snrm2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/snrm2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strsm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strsm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strsm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgelqf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgelqf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgelqf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstein.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstein.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstein.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlascl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlascl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlascl.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 33 [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlagtf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlagtf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlagtf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 45%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasdq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasdq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasdq.c [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarnv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarnv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarnv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 45%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasv2.c.o [ 45%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasv2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasv2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 34 [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slagts.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slagts.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slagts.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarft.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarft.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 46%] [ 46%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstevr.c.o [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrbx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstevr.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrbx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrbx.c [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaruv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaruv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaruv.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgeqrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgeqrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgeqrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 35 [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormlq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormlq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormlq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 47%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorg2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorg2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorg2r.c [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasrt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasrt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasrt.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorgqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlamrg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlamrg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlamrg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd8.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd8.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd8.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slange.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slange.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slange.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormql.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormql.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormql.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 36 [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd3.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetri.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetri.c [ 49%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq1.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasrt2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 49%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaswp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaswp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaswp.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorm2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorm2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorm2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorglq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorglq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorglq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 37 [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorm2l.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorm2l.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorm2l.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd0.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd0.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd0.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 50%] [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd7.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd7.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd7.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorglq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorglq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorglq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaruv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaruv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaruv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 38 [ 50%] [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaev2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaev2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaev2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd0.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd0.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd0.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slabrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slabrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slabrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 52%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sbdsqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sbdsqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsqr.c [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slar1vx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slar1vx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slar1vx.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsqr.c: In function 'sbdsqr_': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsqr.c:61: warning: unused variable 'ftmp' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorgl2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorgl2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorgl2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstegr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstegr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstegr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 39 [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlacpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlacpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlacpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsterf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsterf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsterf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormtr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormtr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormtr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormql.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormql.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormql.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetf2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetf2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetf2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgebd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgebd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgebd2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 40 [ 53%] [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasda.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasda.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasda.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgebrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgebrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgebrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsteqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsteqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsteqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 54%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsyevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsyevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsyevr.c [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasdt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasdt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasdt.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstegr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstegr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstegr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstein.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstein.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstein.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slacpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slacpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slacpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 41 [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssytd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssytd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssytd2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrvx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrvx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrvx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlas2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlas2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlas2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrbx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrbx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrbx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 56%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq5.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasv2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasv2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasv2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaed6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaed6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaed6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 42 [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slartg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slartg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slartg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd4.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorgbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorml2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorml2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorml2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssterf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssterf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssterf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorgbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorgbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorgbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarnv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarnv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarnv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 43 [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ilasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ilasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ilasrt2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgl2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgl2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorgl2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgesdd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgesdd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgesdd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorgqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorgqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorgqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 58%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasrt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasrt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasrt.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaset.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaset.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaset.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 44 [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq4.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlae2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlae2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlae2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 60%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsytrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsytrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsytrd.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sbdsdc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sbdsdc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsdc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dtrtri.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dtrtri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dtrtri.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 45 [ 61%] [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstebz.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaswp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaswp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaswp.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 61%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarfg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarfg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarfg.c [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaev2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaev2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaev2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 61%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq2.c.o [ 61%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq2.c [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slascl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slascl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slascl.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slapy2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slapy2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slapy2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dtrti2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dtrti2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dtrti2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slassq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slassq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slassq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 46 [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq4.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetf2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetf2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetf2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd7.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd7.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd7.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaed6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaed6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaed6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 47 [ 64%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssytrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssytrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssytrd.c [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgelq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgelq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgelq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 64%] [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorm2r.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd5.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorm2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorm2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 64%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlansy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlansy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlansy.c [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasdq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasdq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasdq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 48 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 65%] [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlanst.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlanst.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlanst.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsytd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsytd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsytd2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 65%] [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd8.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd8.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd8.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 65%] [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlatrd.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetri.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetri.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlatrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlatrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarfb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarfb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarfb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 49 [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssteqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssteqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssteqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slatrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slatrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slatrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorml2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorml2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorml2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlabrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlabrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlabrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgeqr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgeqr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgeqr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq3.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 50 [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasda.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasda.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasda.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 68%] [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasr.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaset.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaset.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaset.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slamrg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slamrg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slamrg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/strti2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/strti2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/strti2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgeqrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgeqrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgeqrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 68%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlartg.c.o [ 68%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlartg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlartg.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dbdsqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dbdsqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 51 [ 69%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd2.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c: In function 'dbdsqr_': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c:61: warning: unused variable 'ftmp' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 69%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgebd2.c.o [ 69%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgebd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgebd2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 69%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasdt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasdt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasdt.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 69%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrfx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrfx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrfx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 69%] [ 69%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlange.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlange.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlange.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 52 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgelq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgelq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgelq2.c [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarfb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarfb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarfb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssyevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssyevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssyevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasrt2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlar1vx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlar1vx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlar1vx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 71%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 53 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slagtf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slagtf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slagtf.c [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slas2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slas2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slas2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 72%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slansy.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd3.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slansy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slansy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 72%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarf.c [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorg2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorg2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorg2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetrs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetrs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetrs.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 54 [ 73%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlapy2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlapy2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlapy2.c [ 73%] [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dbdsdc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dbdsdc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsdc.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd4.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/strtri.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/strtri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/strtri.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 55 [ 75%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormlq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormlq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormlq.c [ 75%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgesdd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgesdd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgesdd.c [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq3.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrvx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrvx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrvx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrfx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrfx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrfx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetrs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetrs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetrs.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlassq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlassq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlassq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slae2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slae2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slae2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 56 [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 76%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorm2l.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorm2l.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorm2l.c [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarfg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgebrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlagts.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlagts.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlagts.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormtr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 57 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 78%] [ 78%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq6.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slanst.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slanst.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slanst.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 78%] [ 78%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgeqr2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgelqf.c Linking C shared library libgmx_openmpi.so cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/gmxlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 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/usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 [ 78%] Built target gmx make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/depend make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/openmpi-single /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib/CMakeFiles/md.dir/depend.internal". Scanning dependencies of target md make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/build make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 78%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 78%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 58 [ 78%] Building C object src/mdlib/CMakeFiles/md.dir/mdatom.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdatom.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c Building C object src/mdlib/CMakeFiles/md.dir/sim_util.c.o [ 79%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/sim_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_mkl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_mkl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_mkl.c Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall_sse2_single.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdebin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c: In function 'init_mdatoms': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:55: warning: unused variable 'ilist' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'nmol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'mb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'calc_virial': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:362: warning: unused variable 'virtest' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:361: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'init_mdebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:544: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:136: warning: unused variable 'nh' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'finish_run': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1358: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'upd_mdebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:650: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'init_md': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1467: warning: unused variable 'mod' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1467: warning: unused variable 'tmpt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1466: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1466: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'print_ebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:929: warning: unused variable 'enxlambda_data' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:918: warning: unused variable 'nor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:918: warning: unused variable 'ndr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/coupling.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/coupling.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/qm_orca.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_orca.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'NHC_trotter': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:62: warning: unused variable 'jmax' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'boxv_trotter': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:184: warning: unused variable 'Winvm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:183: warning: unused variable 'T' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'berendsen_pcoupl': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:446: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'trotter_update': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:660: warning: unused variable 'consk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:657: warning: unused variable 'dumvir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:657: warning: unused variable 'dumpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'nd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'kT' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'reft' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'qmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'bmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'dvdlcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'pcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'ecorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:651: warning: unused variable 'ntgrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:651: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'init_npt_vars': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:784: warning: unused variable 'dumvir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:784: warning: unused variable 'dumpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:783: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'dvdlcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'pcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'ecorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:780: warning: unused variable 'tcstat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:779: warning: unused variable 'gc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:779: warning: unused variable 'ntgrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'NPT_energy': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'Q' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'W' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'dbaro' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:998: warning: unused variable 'tau' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:998: warning: unused variable 'eta' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'ngtcall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'qmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'bmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c: In function 'read_orca_output': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c:263: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftw3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftw3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw3.c /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/partdec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/partdec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/iteratedconstraints.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/iteratedconstraints.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'gmx_tx': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:101: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:100: warning: unused variable 'flag' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'init_partdec_constraint': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:508: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'init_partdec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:563: warning: unused variable 'nodeid' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'create_vsitelist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:769: warning: unused variable 'minidx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'setup_parallel_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:831: warning: unused variable 'recvbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:831: warning: unused variable 'sendbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:765: warning: 'create_vsitelist' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c: In function 'done_iterating': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c:103: warning: unused variable 'xmin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 59 [ 80%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftw2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftw2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 80%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_double.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_sse2_double.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_sse2_double.c [ 80%] [ 80%] Building C object src/mdlib/CMakeFiles/md.dir/vsite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/vsite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c Building C object src/mdlib/CMakeFiles/md.dir/qmmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qmmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'constr_vsiten': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:376: warning: unused variable 'xs' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'construct_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'rtmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'vtmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'reftmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:417: warning: unused variable 'ii' [ 80%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite2': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:588: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite3FD': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:703: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fx' Building C object src/mdlib/CMakeFiles/md.dir/rf_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/rf_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite_f': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1188: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'count_intercg_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1344: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'get_vsite_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1383: warning: unused variable 'cg_c' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'init_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1494: warning: unused variable 'cg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c: In function 'update_QMMMrec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c:740: warning: unused variable 'MMatoms' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c:140: warning: 'int_comp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c: In function 'RF_excl_correction': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c:58: warning: unused variable 'top' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 80%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_box.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_box.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_box.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 80%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_parallel_3dfft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c:46: warning: 'copy_int_array' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c:57: warning: 'make_slab2grid' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 60 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 82%] [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/pppm.c.o Building C object src/mdlib/CMakeFiles/md.dir/shellfc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/shellfc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pppm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c: In function 'gmx_pppm_init': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:508: warning: unused variable 'spacing' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:508: warning: unused variable 'box_diag' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:507: warning: unused variable 'tol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:506: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:506: warning: unused variable 'r1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:505: warning: unused variable 'grids' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'porder' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'nz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'nx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'predict_shells': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:118: warning: unused variable 'dt_3' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:118: warning: unused variable 'dt_2' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'init_shell_flexcon': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:200: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'init_adir': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:689: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:689: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:686: warning: unused variable 'scale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'gt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'ga' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'gf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'relax_shell_flexcon': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:777: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:772: warning: unused variable 'xiS' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:772: warning: unused variable 'xiH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:770: warning: unused variable 'dx' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/minimize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/minimize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'get_f_norm_max': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:185: warning: unused variable 'fmax2_0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:909: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:895: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:894: warning: unused variable 'sfm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_lbfgs': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:1431: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_steep': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2059: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2049: warning: unused variable 'dvdlambda' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2048: warning: unused variable 'constepsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_nm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2269: warning: unused variable 'fmax' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2269: warning: unused variable 'fnorm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2255: warning: unused variable 'bNS' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:569: warning: 'do_x_step' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:591: warning: 'do_x_sub' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/shakef.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/shakef.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'cshake': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tiz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tiy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tix' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'vec_shakef': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'rvscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'rscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'vscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'crattle': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tiz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tiy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tix' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'jmdt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'imdt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'diff' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'rijd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:456: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:454: warning: unused variable 'mytol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:83: warning: 'pv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/md_support.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/md_support.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/ebin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ebin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c: In function 'add_ebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:127: warning: unused variable 'sigma' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:127: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c: At top level: [ 82%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c: In function 'compute_globals': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:297: warning: unused variable 'temp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:297: warning: unused variable 'ekin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:294: warning: unused variable 'bVV' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:293: warning: unused variable 'shakeall_vir' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:54: warning: 'rms_ener' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall_sse2_double.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/vcm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/vcm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 61 [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/fft5d.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/fft5d.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/fft5d.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'calc_vcm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'zz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'yz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'yy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'do_stopcm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:170: warning: unused variable 'tm_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:170: warning: unused variable 'tm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:169: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'check_cm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:249: warning: unused variable 'Tcm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/fft5d.c:115: warning: 'lpfactor' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/constr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/constr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/perf_est.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/perf_est.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'too_many_constraint_warnings': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:185: warning: unused variable 'abort' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'constrain': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:306: warning: unused variable 'vstor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:304: warning: unused variable 'ncons' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:303: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c: In function 'pme_load_estimate': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c:91: warning: unused variable 'fljtab' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'init_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:955: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'inter_charge_group_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:1120: warning: unused variable 'nat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:163: warning: 'icomp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/nsgrid.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/nsgrid.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'set_grid_sizes': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:206: warning: unused variable 'stddev' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:206: warning: unused variable 'av' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'init_grid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:361: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:361: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'grid_first': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:474: warning: unused variable 'cx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/wnblist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/wnblist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: In function 'read_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'icmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'full' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'nnbl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:136: warning: unused variable 'b2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:136: warning: unused variable 'b1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:135: warning: unused variable 'bNL' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: In function 'dump_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:234: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mvxvf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mvxvf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/pme_pp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pme_pp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme_pp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 62 [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ewald.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c: In function 'init_ewald_tab': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c:105: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/edsam.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/edsam.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/edsam.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/qm_gamess.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_gamess.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_gamess.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_xml.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_qhop_xml.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftpack.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftpack.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftpack.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used [ 84%] [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_network.c.o Building C object src/mdlib/CMakeFiles/md.dir/csettle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/csettle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_network.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_network.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'qhop_process_attr': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:182: warning: unused variable 'eprop' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'qhop_process_tree': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:247: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'gmx_qhops_read': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:279: warning: unused variable 'npd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:279: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'add_xml_qhop': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:311: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:310: warning: unused variable 'comp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:310: warning: unused variable 'grandchild' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'gmx_qhops_write': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:333: warning: unused variable 'nmt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'settle_proj': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:189: warning: unused variable 'kfacHH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:189: warning: unused variable 'kfacOH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:188: warning: unused variable 'invvscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:187: warning: unused variable 'derpm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'xshake': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:305: warning: unused variable 'conv' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'csettle': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:417: warning: unused variable 'shakeret' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 63 [ 86%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/mdlib/CMakeFiles/md.dir/wall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/wall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/genborn.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c: In function 'do_walls': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c:109: warning: unused variable 'Heps' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'init_gb_still': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'rbc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'rab' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'cosine' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'factor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p3' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:205: warning: unused variable 'rk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:205: warning: unused variable 'r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:204: warning: unused variable 'angle' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:204: warning: unused variable 'length' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:202: warning: unused variable 'ibm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:202: warning: unused variable 'iam' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'at' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'idx2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'id' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'ic' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nang' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nbond' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'init_gb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:390: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'ai' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_still': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:518: warning: unused variable 'dr4' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:518: warning: unused variable 'dr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:515: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_hct': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:656: warning: unused variable 'duij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:652: warning: unused variable 'gpi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:649: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:649: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_obc': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:875: warning: unused variable 'duij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:872: warning: unused variable 'min_rad' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:872: warning: unused variable 'rad' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:871: warning: unused variable 'gpi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:868: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:868: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1094: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'gb_bonds_tab': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1346: warning: unused variable 'dvdaj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1346: warning: unused variable 'vcoul' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1339: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_nonpolar': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1477: warning: unused variable 'rbi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_chainrule': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1550: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1548: warning: unused variable 'rinv11' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1547: warning: unused variable 'rsq11' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1546: warning: unused variable 'rb2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1546: warning: unused variable 'fij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_forces': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1663: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1661: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'make_gb_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1887: warning: unused variable 'apa' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1875: warning: 'compare_int' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/forcerec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/forcerec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin_bar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdebin_bar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin_bar.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'check_solvent_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:164: warning: unused variable 'excl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'set_avcsixtwelve': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:769: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'init_forcerec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1299: warning: unused variable 'ngrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1299: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1235: warning: 'forcerec_check_sse2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin_bar.c:99: warning: 'mde_delta_h_free' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/init.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/init.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c: In function 'set_state_entries': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c:73: warning: unused variable 'nnhpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c:64: warning: 'int_title' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_con.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_con.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: In function 'dd_make_local_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c:950: warning: unused variable 'gat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: In function 'init_domdec_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c:1074: warning: unused variable 'dc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/nlistheuristics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/nlistheuristics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nlistheuristics.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 64 [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/clincs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/clincs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: In function 'do_lincsp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'lam' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'wfac' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'rlen' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: In function 'constrain_lincs': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:1165: warning: unused variable 'error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:1114: warning: 'dump_conf' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/tgroup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tgroup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: In function 'init_grptcstat': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c:56: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: In function 'sum_ekin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c:204: warning: unused variable 'ek' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/pull.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pull.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/calcvir.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: In function 'get_pullgrps_dr': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:301: warning: unused variable 'pref' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: In function 'do_constraint': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:458: warning: unused variable 'mass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:457: warning: unused variable 'd0' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_parm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_qhop_parm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_parm.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c:46: warning: 'dprod1' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c:159: warning: 'lo_fcv2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/calcmu.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/calcmu.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcmu.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/groupcoord.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/groupcoord.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/groupcoord.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 65 [ 89%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/stat.c.o /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/stat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/stat.c /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: In function 'setup_gb_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:119: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:116: warning: unused variable 'nj1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:116: warning: unused variable 'nj0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:114: warning: unused variable 'tp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: In function 'genborn_allvsall_setup': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:330: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 89%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used Building C object src/mdlib/CMakeFiles/md.dir/domdec_top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'print_missing_interactions_mb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:114: warning: unused variable 'a_gl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:114: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'global_atomnr_to_moltype_ind': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:364: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'count_excls': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:379: warning: unused variable 'n_inter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_make_reverse_top': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:628: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:628: warning: unused variable 'n_recursive_vsite' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'add_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:772: warning: unused variable 'iatoms_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'make_local_exclusions': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1234: warning: unused variable 'a_loc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_make_local_top': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1422: warning: unused variable 'bUniqueExcl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_init_local_state': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1576: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1576: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'check_link': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1616: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/update.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/update.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/domdec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'do_update_vv_vel': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vnrel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'va' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vv' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vn' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'u' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:237: warning: unused variable 'vrel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:236: warning: unused variable 'gt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:235: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'do_update_vv_pos': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:287: warning: unused variable 'w_dt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:287: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_move_cellx': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:982: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:982: warning: unused variable 'dim1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_collect_vec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1432: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_tcouple': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'homenr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1430: warning: unused variable 'ma' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1303: warning: unused variable 'vbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1298: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1298: warning: unused variable 'bExtended' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_distribute_vec_scatterv':/builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_box': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1470: warning: unused variable 'vir_con' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1469: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1468: warning: unused variable 'dt_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bEner' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bLog' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bLastStep' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1667: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_coords': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xprimein' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xpall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'fall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_distribute_state': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1709: warning: unused variable 'ngtcp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1709: warning: unused variable 'ngtch' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'forcein' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xcom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vcom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1587: warning: unused variable 'vir_con' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1586: warning: unused variable 'icom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nexpand' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nconstr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nsettle' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nshake' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'jatom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'iatom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'blen1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'blen0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1581: warning: unused variable 'imassin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1581: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bEner' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bLog' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bLastStep' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'gmx_ddcoord2pmeindex': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2075: warning: unused variable 'nc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2075: warning: unused variable 'coords_pme' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'make_dd_indices': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2393: warning: unused variable 'ga2la' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'check_bLocalCG': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2449: warning: unused variable 'ncg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'set_dd_cell_sizes_dlb_root': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3183: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'distribute_dd_cell_sizes_dlb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: At top level:/builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3365: warning: unused variable 'dim1' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'distribute_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3657: warning: unused variable 'bUnbounded' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3653: warning: unused variable 'box_size' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3651: warning: unused variable 'npbcdim' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_redistribute_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4177: warning: unused variable 'cell_d' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4177: warning: unused variable 'd4' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'get_load_distribution': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4849: warning: unused variable 'cid' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'setup_dd_grid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:5309: warning: unused variable 'bZYX' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'check_dlb_support': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6039: warning: unused variable 'dd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'init_domain_decomposition': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_init_bondeds': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6694: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6693: warning: unused variable 'bBondComm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'setup_dd_communication': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'inv_ncg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r2inc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_scomm2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_mb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_partition_system': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:8178: warning: unused variable 'j' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_setup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_setup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:291: warning: 'ga2la_get_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'guess_npme': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:145: warning: unused variable 'ir_try' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:144: warning: unused variable 'nky' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:144: warning: unused variable 'nkx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'comm_cost_est': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:298: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'assign_factors': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:486: warning: unused variable 'z' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/ghat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ghat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ghat.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft.c /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 66 [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tables.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/pullutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pullutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'done_tabledata': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:483: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'make_tables': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:868: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'make_gb_table': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:991: warning: unused variable 'x0_r2_error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:991: warning: unused variable 'x0_r_error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:990: warning: unused variable 'rel_error_r2_old' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:990: warning: unused variable 'rel_error_r_old' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:989: warning: unused variable 'rel_error_r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:989: warning: unused variable 'rel_error_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:988: warning: unused variable 'abs_error_r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:988: warning: unused variable 'abs_error_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'tabsel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:977: warning: unused variable 'fns14' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:159: warning: 'splint' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: In function 'pull_set_pbcatom': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c:85: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: In function 'pull_calc_coms': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c:281: warning: unused variable 'xx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/ns.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ns.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'init_neighbor_list': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:248: warning: unused variable 'solvent' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'new_i_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'nshift' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'put_in_list_at': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:640: warning: unused variable 'rlj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:640: warning: unused variable 'qq' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:635: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:633: warning: unused variable 'ind_ij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_inner_tric': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1466: warning: unused variable 'nsbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_inner_rect': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1499: warning: unused variable 'nsbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_simple_core': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'i0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'jcg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'nsgrid_core': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1949: warning: unused variable 'xi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1945: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'init_ns': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2402: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'search_neighbours': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2528: warning: unused variable 'cg_end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2528: warning: unused variable 'cg_start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2527: warning: unused variable 'i_egp_flags' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2526: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2522: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2522: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1637: warning: 'get_dx' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/qm_gaussian.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_gaussian.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_gaussian.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/tpi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tpi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c: In function 'do_tpi': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:160: warning: unused variable 'dvdl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:150: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:150: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:135: warning: unused variable 'TPI' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_mopac.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_mopac.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_wallcycle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_wallcycle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_wallcycle.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 67 [ 91%] Building C object src/mdlib/CMakeFiles/md.dir/pme.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pme.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'pmeredist_pd': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:399: warning: unused variable 'idxa' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'copy_pmegrid_to_fftgrid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:851: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'copy_fftgrid_to_pmegrid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:917: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'spread_q_bsplines': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1105: warning: unused variable 'bndsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1105: warning: unused variable 'localsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1100: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1099: warning: unused variable 'ol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'init_atomcomm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 'nk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'init_overlap_comm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1854: warning: unused variable 'nk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1854: warning: unused variable 'nn' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1853: warning: unused variable 'exten' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'maxlr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'rbnd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'lbnd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'gmx_pme_init': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2039: warning: unused variable 'atc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'gmx_pme_do': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2468: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2464: warning: unused variable 'local_ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'nz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'nx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2004: warning: 'gmx_pme_check_grid_restrictions' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 91%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_single.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_sse2_single.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_sse2_single.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 91%] Building C object src/mdlib/CMakeFiles/md.dir/force.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/force.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: In function 'ns': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:86: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: In function 'do_force_lowlevel': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:147: warning: unused variable 'dvdgb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:141: warning: unused variable 'bDoEpot' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Linking C shared library libmd_openmpi.so cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -shared -Wl,-soname,libmd_openmpi.so.6 -o libmd_openmpi.so.6 CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/iteratedconstraints.c.o CMakeFiles/md.dir/gmx_fft_fftw2.c.o CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/domdec_box.c.o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/pppm.c.o CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/minimize.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/constr.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/nsgrid.c.o CMakeFiles/md.dir/wnblist.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/ewald.c.o CMakeFiles/md.dir/edsam.c.o CMakeFiles/md.dir/qm_gamess.c.o CMakeFiles/md.dir/gmx_qhop_xml.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/wall.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/forcerec.c.o CMakeFiles/md.dir/mdebin_bar.c.o CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/calcvir.c.o CMakeFiles/md.dir/gmx_qhop_parm.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/update.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/ghat.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/pullutil.c.o CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/force.c.o ../gmxlib/libgmx_openmpi.so.6 -ldl -lm -lfftw3f -lxml2 cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/mdlib && /usr/bin/cmake -E cmake_symlink_library libmd_openmpi.so.6 libmd_openmpi.so.6 libmd_openmpi.so make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 58 59 60 61 62 63 64 65 66 67 [ 91%] Built target md make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/depend make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/openmpi-single /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel/CMakeFiles/gmxpreprocess.dir/depend.internal". Scanning dependencies of target gmxpreprocess make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/build make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 91%] [ 91%] [ 91%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/compute_io.c.o Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/add_par.c.o [ 91%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/add_par.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/add_par.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/compute_io.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/convparm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/convparm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gen_ad.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gen_ad.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c: In function 'compute_io': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c:61: warning: unused variable 'nfep' /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'assign_param': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:96: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'new_interaction_list': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:459: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'convert_params': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:469: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:457: warning: 'new_interaction_list' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'get_impropers': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:437: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:436: warning: unused variable 'hbidih' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:434: warning: unused variable 'a0' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'clean_excls': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:576: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:576: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'generate_excls': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'e' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'l1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'k1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'j1' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 91%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:114: warning: 'aeq' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:289: warning: 'ideq' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:327: warning: 'dump_param' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'read_vsite_database': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:150: warning: unused variable 'prevdir' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:150: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'add_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:487: warning: unused variable 'bb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'gen_vsites_trp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:759: warning: unused variable 'c' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:758: warning: unused variable 'mtot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:758: warning: unused variable 'mwtot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:756: warning: unused variable 'xM' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:747: warning: unused variable 'dist' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:746: warning: unused variable 'I' [ 91%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'gen_vsites_tyr': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:986: warning: unused variable 'vmass' Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/genhydro.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/genhydro.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'do_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:1350: warning: unused variable 'bb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 69 [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gpp_atomtype.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'expand_hackblocks_one': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:161: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'check_atoms_present': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:275: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'add_h_low': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:390: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gpp_bond_atomtype.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/h_db.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/h_db.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: In function 'dump_h_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:117: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: In function 'read_h_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:200: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:113: warning: 'dump_h_db' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/hackblock.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/hackblock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hackblock.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/hizzie.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/hizzie.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c: In function 'set_histp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:195: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:192: warning: unused variable 'his0' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:192: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:188: warning: unused variable 'bHaveH' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/nm2type.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/nm2type.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: In function 'rd_nm2type_file': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c:72: warning: unused variable 'blen' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: In function 'nm2type': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c:179: warning: unused variable 'quality' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/pdb2top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/pdb2top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 70 [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/pgutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/pgutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pgutil.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'missing_atoms': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:85: warning: unused variable 'bRet' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'print_top_comment': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:539: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'get_hackblocks_rtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:983: warning: unused variable 'bC' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:983: warning: unused variable 'bN' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:981: warning: unused variable 'Hnum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:980: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'match_atomnames_with_rtp_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1160: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'match_atomnames_with_rtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1324: warning: unused variable 'bFoundInAdd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1323: warning: unused variable 'start_nr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1322: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1322: warning: unused variable 'start_at' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1321: warning: unused variable 'anmnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1320: warning: unused variable 'hbr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1317: warning: unused variable 'newnm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1316: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'gen_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1354: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1354: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:743: warning: 'inter_res_bond' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/readir.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/readir.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/readpull.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/readpull.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'check_ir': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:162: warning: unused variable 'ns_type' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'do_index': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:1782: warning: unused variable 'SAtime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'triple_check': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:2293: warning: unused variable 'npct' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c: In function 'read_pullparams': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c:107: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c:103: warning: unused variable 'nchar' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/resall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/resall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c: In function 'read_resall': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c:256: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c:482: warning: 'neq_str' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/sorting.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/sorting.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/sorting.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/specbond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/specbond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/specbond.c /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/ter_db.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/ter_db.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/tomorse.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/tomorse.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tomorse.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'read_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:84: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'print_ter_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:136: warning: unused variable 'nname' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'filter_ter': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:375: warning: unused variable 's2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:373: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 71 [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topdirs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topdirs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topdirs.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topexcl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topexcl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c: In function 'generate_excl': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/toppush.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/toppush.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: In function 'generate_gb_exclusion_interactions': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n14' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n13' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:389: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:389: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: In function 'read_topol': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:517: warning: unused variable 'block' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_nbt': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:794: warning: unused variable 'sig6' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:792: warning: unused variable 'atnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:787: warning: unused variable 'form2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_cmaptype': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:920: warning: unused variable 'bAllowRepeat' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:915: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'default_cmap_params': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1312: warning: unused variable 'j' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_bond': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1485: warning: unused variable 'paramB' [ 95%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'param_defB' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'param_defA' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'paramB' Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topshake.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topshake.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c: In function 'make_shake': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c:98: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c:98: warning: unused variable 'nb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/toputil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/toputil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toputil.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toputil.c:175: warning: 'print_nbt' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_block': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_blocka': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:321: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:320: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_top': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_groups': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:376: warning: unused variable 'ndiff' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'comp_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:715: warning: unused variable 'sh' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'comp_enx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:1048: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:1045: warning: unused variable 'block' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 72 [ 97%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'vsitetype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_angles': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'vsitetype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_dihs': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'ftype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 97%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/fflibutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/fflibutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c: In function 'low_fflib_search_file_end': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:159: warning: unused variable 'pdum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:153: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:151: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 97%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/xlate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/xlate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xlate.c /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used Linking C shared library libgmxpreprocess_openmpi.so cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -shared -Wl,-soname,libgmxpreprocess_openmpi.so.6 -o libgmxpreprocess_openmpi.so.6 CMakeFiles/gmxpreprocess.dir/add_par.c.o CMakeFiles/gmxpreprocess.dir/compute_io.c.o CMakeFiles/gmxpreprocess.dir/convparm.c.o CMakeFiles/gmxpreprocess.dir/gen_ad.c.o CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o CMakeFiles/gmxpreprocess.dir/genhydro.c.o CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o CMakeFiles/gmxpreprocess.dir/h_db.c.o CMakeFiles/gmxpreprocess.dir/hackblock.c.o CMakeFiles/gmxpreprocess.dir/hizzie.c.o CMakeFiles/gmxpreprocess.dir/nm2type.c.o CMakeFiles/gmxpreprocess.dir/pdb2top.c.o CMakeFiles/gmxpreprocess.dir/pgutil.c.o CMakeFiles/gmxpreprocess.dir/readir.c.o CMakeFiles/gmxpreprocess.dir/readpull.c.o CMakeFiles/gmxpreprocess.dir/resall.c.o CMakeFiles/gmxpreprocess.dir/sorting.c.o CMakeFiles/gmxpreprocess.dir/specbond.c.o CMakeFiles/gmxpreprocess.dir/ter_db.c.o CMakeFiles/gmxpreprocess.dir/tomorse.c.o CMakeFiles/gmxpreprocess.dir/topdirs.c.o CMakeFiles/gmxpreprocess.dir/topexcl.c.o CMakeFiles/gmxpreprocess.dir/topio.c.o CMakeFiles/gmxpreprocess.dir/toppush.c.o CMakeFiles/gmxpreprocess.dir/topshake.c.o CMakeFiles/gmxpreprocess.dir/toputil.c.o CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o CMakeFiles/gmxpreprocess.dir/fflibutil.c.o CMakeFiles/gmxpreprocess.dir/xlate.c.o ../mdlib/libmd_openmpi.so.6 ../gmxlib/libgmx_openmpi.so.6 -ldl -lm -lfftw3f -lxml2 cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/bin/cmake -E cmake_symlink_library libgmxpreprocess_openmpi.so.6 libgmxpreprocess_openmpi.so.6 libgmxpreprocess_openmpi.so make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 69 70 71 72 [ 97%] Built target gmxpreprocess make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/depend make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/openmpi-single /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel/CMakeFiles/mdrun.dir/depend.internal". Scanning dependencies of target mdrun make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/build make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 97%] [ 97%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 73 [ 98%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles Building C object src/kernel/CMakeFiles/mdrun.dir/ionize.c.o Building C object src/kernel/CMakeFiles/mdrun.dir/gctio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/gctio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gctio.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/ionize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ionize.c [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/runner.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/runner.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c Building C object src/kernel/CMakeFiles/mdrun.dir/do_gct.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/do_gct.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: In function 'init_coupling': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:62: warning: unused variable 'atj' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:62: warning: unused variable 'ati' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'index' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'nc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: In function 'do_coupling': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:493: warning: unused variable 'bTest' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:491: warning: unused variable 'xi12'/builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c: In function 'mdrunner': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:368: warning: unused variable 'nthreads' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:367: warning: unused variable 'cr_old' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:362: warning: unused variable 'list' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:359: warning: unused variable 'gro' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:348: warning: unused variable 'tmpr2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:348: warning: unused variable 'tmpr1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:342: warning: unused variable 'realtime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:342: warning: unused variable 'nodetime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:491: warning: unused variable 'xi6' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffa' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:489: warning: unused variable 'rmsf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:461: warning: 'dump_fm' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/repl_ex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/repl_ex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: In function 'init_replica_exchange': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:118: warning: unused variable 'temp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: In function 'replica_exchange': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:725: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:706: warning: 'write_debug_x' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/xutils.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/xutils.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/md.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/md.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c: In function 'update_forcefield': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c:334: warning: unused variable 'bDone' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c: In function 'do_md': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:184: warning: unused variable 'iter_i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:179: warning: unused variable 'oldfom' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:179: warning: unused variable 'fom' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:178: warning: unused variable 'tmpvir' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:174: warning: unused variable 'grpname' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:164: warning: unused variable 'timestep' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:140: warning: unused variable 'ebox' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:140: warning: unused variable 'scale_tot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/mdrun.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/mdrun.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/genalg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/genalg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:551: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:503: warning: unused variable 'fptest' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:498: warning: unused variable 'ed' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:387: warning: unused variable 'bPPPME' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:386: warning: unused variable 'bCart' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c: In function 'update_ga': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c:196: warning: unused variable 'j' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 74 [100%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/md_openmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c: In function 'do_md_openmm': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c:151: warning: unused variable 'reset_counters_now' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c:151: warning: unused variable 'reset_counters' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Linking C executable mdrun cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC CMakeFiles/mdrun.dir/gctio.c.o CMakeFiles/mdrun.dir/ionize.c.o CMakeFiles/mdrun.dir/runner.c.o CMakeFiles/mdrun.dir/do_gct.c.o CMakeFiles/mdrun.dir/repl_ex.c.o CMakeFiles/mdrun.dir/xutils.c.o CMakeFiles/mdrun.dir/md.c.o CMakeFiles/mdrun.dir/mdrun.c.o CMakeFiles/mdrun.dir/genalg.c.o CMakeFiles/mdrun.dir/md_openmm.c.o -o mdrun -rdynamic -ldl -lm libgmxpreprocess_openmpi.so.6 ../mdlib/libmd_openmpi.so.6 ../gmxlib/libgmx_openmpi.so.6 -ldl -lm -lfftw3f -lxml2 make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 73 74 [100%] Built target mdrun make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/openmpi-single/CMakeFiles 0 make[1]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-single' + cd .. + SUFFIXCONF='-D GMX_DEFAULT_SUFFIX=OFF -D GMX_BINARY_SUFFIX= -D GMX_LIBS_SUFFIX=_openmpi_d' + mkdir openmpi-double + cd openmpi-double + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + export FFLAGS + /usr/bin/cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DCMAKE_SKIP_RPATH:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=ON -D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=lib64 -D GMX_DOUBLE=ON -D GMX_MPI=ON -D GMX_DEFAULT_SUFFIX=OFF -D GMX_BINARY_SUFFIX= -D GMX_LIBS_SUFFIX=_openmpi_d .. -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/lib64/openmpi/bin/mpicc -- Check for working C compiler: /usr/lib64/openmpi/bin/mpicc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/lib64/openmpi/bin/mpicxx -- Check for working CXX compiler: /usr/lib64/openmpi/bin/mpicxx -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Failed -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Failed -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Using manually set binary suffix: "" -- Using manually set library suffix: "_openmpi_d" WARNING There are known problems with some MPI implementations: OpenMPI version < 1.4.1 MVAPICH2 version <= 1.4.1 * -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Checking for CRAY XT Catamount compile -- Checking for CRAY XT Catamount target - no -- Looking for include files HAVE_STRING_H -- Looking for include files HAVE_STRING_H - found -- Looking for include files HAVE_MATH_H -- Looking for include files HAVE_MATH_H - found -- Looking for include files HAVE_LIMITS_H -- Looking for include files HAVE_LIMITS_H - found -- Looking for include files HAVE_MEMORY_H -- Looking for include files HAVE_MEMORY_H - found -- Looking for include files HAVE_UNISTD_H -- Looking for include files HAVE_UNISTD_H - found -- Looking for include files HAVE_DIRECT_H -- Looking for include files HAVE_DIRECT_H - not found. -- Looking for include files HAVE_PWD_H -- Looking for include files HAVE_PWD_H - found -- Looking for include files HAVE_STDINT_H -- Looking for include files HAVE_STDINT_H - found -- Looking for include files HAVE_STDLIB_H -- Looking for include files HAVE_STDLIB_H - found -- Looking for include files HAVE_PTHREAD_H -- Looking for include files HAVE_PTHREAD_H - found -- Looking for include files HAVE_DIRENT_H -- Looking for include files HAVE_DIRENT_H - found -- Looking for include files HAVE_INTTYPES_H -- Looking for include files HAVE_INTTYPES_H - found -- Looking for include files HAVE_REGEX_H -- Looking for include files HAVE_REGEX_H - found -- Looking for include files HAVE_SYS_TYPES_H -- Looking for include files HAVE_SYS_TYPES_H - found -- Looking for include files HAVE_SYS_STAT_H -- Looking for include files HAVE_SYS_STAT_H - found -- Looking for include files HAVE_SYS_TIME_H -- Looking for include files HAVE_SYS_TIME_H - found -- Looking for include files HAVE_RPC_RPC_H -- Looking for include files HAVE_RPC_RPC_H - found -- Looking for include files HAVE_RPC_XDR_H -- Looking for include files HAVE_RPC_XDR_H - found -- Looking for include files HAVE_XMMINTRIN_H -- Looking for include files HAVE_XMMINTRIN_H - not found. -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - not found. -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include files HAVE_PMMINTRIN_H - not found. -- Looking for include files HAVE_SMMINTRIN_H -- Looking for include files HAVE_SMMINTRIN_H - not found. -- Looking for include files HAVE_IO_H -- Looking for include files HAVE_IO_H - not found. -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strdup -- Looking for strdup - found -- Looking for vprintf -- Looking for vprintf - found -- Looking for memcmp -- Looking for memcmp - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Looking for _aligned_malloc -- Looking for _aligned_malloc - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for isnan -- Looking for isnan - found -- Looking for _isnan -- Looking for _isnan - not found -- Looking for isfinite -- Looking for isfinite - not found -- Looking for _isfinite -- Looking for _isfinite - not found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for cbrt in m -- Looking for cbrt in m - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of bool -- Check size of bool - failed -- Check size of int -- Check size of int - done -- Check size of long int -- Check size of long int - done -- Check size of long long int -- Check size of long long int - done -- Check size of off_t -- Check size of off_t - done -- Check size of void * -- Check size of void * - done -- Check size of uid_t -- Check size of uid_t - done -- Check size of gid_t -- Check size of gid_t - done -- Check size of size_t -- Check size of size_t - done -- Check size of off_t -- Check size of off_t - done -- Check if the system is big endian -- Searching 16 bit integer -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - big endian -- checking for module 'libxml-2.0' -- found libxml-2.0, version 2.7.6 -- Found LibXml2: /usr/lib64/libxml2.so -- Setting build user & time -- Setting build user & time - OK -- Checking floating point format -- Checking floating point format - unknown -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for return type of signals -- Checking for return type of signals - void -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for inline keyword -- Checking for inline keyword - inline -- Checking for inline keyword -- Checking for inline keyword - inline -- Checking for pipe support -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Checking for MSVC x86 inline asm -- Checking for MSVC x86 inline asm - not supported -- Checking for system XDR support -- Checking for system XDR support - present -- Found FFTW3: /usr/lib64/libfftw3.so -- Found assembler: /usr/bin/as -- Loaded CMakeASM-ATTInformation - ASM-ATT support is still experimental, please report issues -- Configuring done -- Generating done -- Build files have been written to: /builddir/build/BUILD/gromacs-4.5.5/openmpi-double + make VERBOSE=1 -j4 mdrun /usr/bin/cmake -H/builddir/build/BUILD/gromacs-4.5.5 -B/builddir/build/BUILD/gromacs-4.5.5/openmpi-double --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 mdrun make[1]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -H/builddir/build/BUILD/gromacs-4.5.5 -B/builddir/build/BUILD/gromacs-4.5.5/openmpi-double --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 73 make -f CMakeFiles/Makefile2 src/kernel/CMakeFiles/mdrun.dir/all make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/depend make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/openmpi-double /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib/CMakeFiles/gmx.dir/depend.internal". Scanning dependencies of target gmx make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/build make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 0%] [ 0%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_fatal.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/princ.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/princ.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c [ 0%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_fatal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_fatal.c Building C object src/gmxlib/CMakeFiles/gmx.dir/topsort.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/topsort.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c Building C object src/gmxlib/CMakeFiles/gmx.dir/random.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/random.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c: In function 'gmx_sort_ilist_fe': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/topsort.c:185: warning: unused variable 'bPert' /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_fatal.c:150: warning: 'bputi' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c: In function 'maxwell_speed': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c:93: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c:92: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/random.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c:48: warning: 'm_op' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/princ.c:249: warning: 'dump_shit' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/checkpoint.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/checkpoint.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/dihres.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/dihres.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_cyclecounter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_cyclecounter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_cyclecounter.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 1 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_real': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:448: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_ints': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:459: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_doubles': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:526: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpte_rvecs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:591: warning: unused variable 'n3' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpt_header': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:700: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'do_cpt_files': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1043: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'write_checkpoint': [ 1%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1159: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1154: warning: unused variable 'flag_64bit' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'read_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:1459: warning: unused variable 'filename' Building C object src/gmxlib/CMakeFiles/gmx.dir/warninp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/warninp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/warninp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: In function 'list_checkpoint': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2001: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2001: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:2000: warning: unused variable 'indent' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/checkpoint.c:429: warning: 'do_cpte_reals' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sfactor.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sfactor.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sfactor.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c: In function 'ta_dihres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c:78: warning: unused variable 'dp2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c:77: warning: unused variable 'typep' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/dihres.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ifunc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ifunc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ifunc.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ffscanf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ffscanf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ffscanf.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_system_xdr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_system_xdr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_system_xdr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/macros.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/macros.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/macros.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/shift_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/shift_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 2 [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/atomprop.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/atomprop.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c: In function 'shift_LRcorrection': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:271: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:267: warning: unused variable 'qtot' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:266: warning: unused variable 'isp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:44: warning: 'tMPI_Atomic_add_return' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_intrinsics.h:49: warning: 'tMPI_Atomic_fetch_add' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:55: warning: 'tMPI_Spinlock_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:61: warning: 'tMPI_Spinlock_lock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:79: warning: 'tMPI_Spinlock_trylock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:85: warning: 'tMPI_Spinlock_unlock' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:90: warning: 'tMPI_Spinlock_islocked' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic/gcc_spinlock.h:96: warning: 'tMPI_Spinlock_wait' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:642: warning: 'tMPI_Atomic_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/thread_mpi/atomic.h:661: warning: 'tMPI_Atomic_ptr_swap' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/shift_util.c:384: warning: 'rgbset' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c: In function 'gmx_atomprop_init': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c:246: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/atomprop.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrnb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrnb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrnb.c /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/tpxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/tpxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/calch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/calch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_pullgrp': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:212: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c: In function 'gen_waterhydrogen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c:82: warning: unused variable 'kkk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calch.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_iparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:931: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ilist': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1179: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1200: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_ilists': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1262: warning: unused variable 'bDum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1261: warning: unused variable 'renum' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1261: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_grps': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1382: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1498: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1498: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_atomtypes': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1525: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_moltype': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1678: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_molblock': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1706: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_mtop': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:1834: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'do_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2046: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'read_tpx_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2347: warning: unused variable 'ltop' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: In function 'read_tps_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c:2376: warning: unused variable 'topconv' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 2%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tpxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/wman.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/wman.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'mydate': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:202: warning: unused variable 'num' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'print_tty_formatted': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:551: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_wikiman': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:672: warning: unused variable 'tmp2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:671: warning: unused variable 'link' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_htmlman': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:723: warning: unused variable 'link' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: In function 'write_py': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c:966: warning: unused variable 'bHidden' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wman.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/string2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/string2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c: In function 'ltrim': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/string2.c:137: warning: unused variable 'tr' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/matio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/matio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c: In function 'write_xpm_map_split': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'fac' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:662: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c:661: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 3 [ 4%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/matio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/pargs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pargs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c: In function 'print_pargs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'buf2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c:330: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pargs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_asc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_asc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_asc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/index.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/index.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'analyse_prot': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:365: warning: unused variable 'nnpres' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'gmx_residuetype_add': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:514: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'gmx_residuetype_init': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:546: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:545: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: In function 'analyse': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:734: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c:732: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/index.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xtcio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xtcio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xtcio.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pdbio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pdbio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: In function 'gmx_conect_add': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:681: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: In function 'read_pdbfile': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:705: warning: unused variable 'chidmax' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c:704: warning: unused variable 'nres_ter_prev' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pdbio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 4%] Building C object src/gmxlib/CMakeFiles/gmx.dir/readinp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/readinp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 4%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: In function 'get_einp': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c:283: warning: unused variable 'warn_buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: In function 'get_eenum': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c:456: warning: unused variable 'dum' Building C object src/gmxlib/CMakeFiles/gmx.dir/main.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/main.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/readinp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'par_fn': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:140: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'gmx_log_open': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:259: warning: unused variable 'testlen' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'init_multisystem': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:485: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: In function 'init_par': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c:522: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 4 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/main.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used [ 5%] /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/orires.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/orires.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c: In function 'init_orires': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c:58: warning: unused variable 'nr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/orires.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/calcgrid.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/calcgrid.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sortwater.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sortwater.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sortwater.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c: In function 'calc_grid': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/calcgrid.c:98: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/pbc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/pbc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'set_default_time_unit': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:255: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'set_default_xvg_format': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:287: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:286: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: In function 'parse_common_args': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:578: warning: unused variable 'envstr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:577: warning: unused variable 'newdesc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:577: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:536: warning: unused variable 'npri_pa' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:529: warning: unused variable 'mantp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statutil.c:409: warning: 'pdesc' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'low_set_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:285: warning: unused variable 'bXY' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'put_atom_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1195: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: In function 'put_atoms_in_box': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1209: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c:1209: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/pbc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trnio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trnio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trnio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 5%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_remove': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:339: warning: unused variable 'prev' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_open': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:438: warning: unused variable 'xdrid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:435: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_fopen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:640: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_fclose': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:654: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_int_get_file_position': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:783: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_get_output_file_positions': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:858: warning: unused variable 'ret' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:837: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:835: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:834: warning: unused variable 'pos_lo' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:834: warning: unused variable 'pos_hi' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:833: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:833: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c: In function 'gmx_fio_int_fsync': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c:1005: warning: unused variable 'filen' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 5 [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/maths.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/maths.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c: In function 'gmx_erfc': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 'z4' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 'z2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 's3' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 's2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 's1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 'r2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c:302: warning: unused variable 'r1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/maths.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mtxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 6%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: In function 'gmx_mtxio_write': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c:92: warning: unused variable 'bRead' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: In function 'gmx_mtxio_read': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c:166: warning: unused variable 'bRead' Building C object src/gmxlib/CMakeFiles/gmx.dir/xvgr.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xvgr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/libxdrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/libxdrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 6%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'xvgropen_type': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:287: warning: unused variable 't' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'fgets3': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:442: warning: unused variable 'p' Building C object src/gmxlib/CMakeFiles/gmx.dir/replace.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/replace.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/replace.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'read_xvg_legend': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:546: warning: unused variable 'ptr1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:546: warning: unused variable 'ptr0' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: In function 'read_xvg_time': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c:697: warning: unused variable 'tend' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xvgr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr3dfcoord': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:820: warning: unused variable 'xdrid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xtc_get_next_frame_start': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1546: warning: unused variable 'inp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr_xtc_seek_time': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1693: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: In function 'xdr_xtc_get_last_frame_number': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c:1882: warning: unused variable 'res' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/libxdrf.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/viewit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/viewit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/viewit.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/strdb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/strdb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/strdb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/enxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/enxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 6 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 8%] [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/splitter.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/splitter.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c Building C object src/gmxlib/CMakeFiles/gmx.dir/filenm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/filenm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'do_enxnms': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:392: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'do_eheader': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:448: warning: unused variable 'tempfix_nr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:446: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'open_enx': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:723: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: In function 'get_enx_state': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:1071: warning: unused variable 'pcouplmu_nm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/enxio.c:375: warning: 'gen_units' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_force2': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:116: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'mk_border': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:346: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_blocks': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:424: warning: unused variable 'bSHK' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:420: warning: unused variable 'last_shk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:419: warning: unused variable 'ai' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:419: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'merge_sid': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:662: warning: unused variable 'nChanged' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'gen_sblocks': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:760: warning: unused variable 'isid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'istart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:758: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'find_constraint_range_recursive': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:866: warning: unused variable 'nconstr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'pd_determine_constraints_range': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:890: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:890: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: In function 'split_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'minidx' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'ihome' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:933: warning: unused variable 'minhome' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:932: warning: unused variable 'ia' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nrd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nra' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'nvsite_constr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:931: warning: unused variable 'ftype' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'nodeid' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'bstart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'send' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'sstart' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'maxatom' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'atom' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'mj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:928: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: In function 'set_default_file_name': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c:216: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/splitter.c:832: warning: 'block2blocka' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: In function 'add_suffix_to_output_names': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c:951: warning: unused variable 'pos' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/filenm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rmpbc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rmpbc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rmpbc.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/inputrec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/inputrec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/inputrec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rando.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rando.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rando.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 8%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/bondfree.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c [ 8%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trxio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trxio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 7 [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/vmddlopen.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmddlopen.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'FENE_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:242: warning: unused variable 'dr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'do_1_thole': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:652: warning: unused variable 'r12n' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'posres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1254: warning: unused variable 'ki' [ 9%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'cmap_dihs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1642: warning: unused variable 'psi2' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1641: warning: unused variable 'psi1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:1637: warning: unused variable 'l4' Building C object src/gmxlib/CMakeFiles/gmx.dir/txtdump.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/txtdump.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'bonded_tab': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2350: warning: unused variable 'f' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2350: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: In function 'tab_angles': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c:2475: warning: unused variable 'snt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/bondfree.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c: In function 'choose_ff': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c:441: warning: unused variable 'eFF' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trxio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_qm_opts': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:340: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:991: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_block_title': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1037: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_blocka_title': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1050: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_block': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1103: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_atom': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1225: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1260: warning: unused variable 'grpnr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: In function 'pr_header': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1423: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/txtdump.c:1063: warning: 'low_pr_block' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/writeps.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/writeps.c /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxcpp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxcpp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: In function 'cpp_open_file': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c:188: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c: In function 'cpp_close_file': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxcpp.c:577: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_xdr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_xdr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_xdr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 9%] [ 9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_matrix.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/sighandler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sighandler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sighandler.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_matrix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: In function 'free_matrix': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c:63: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: In function 'multi_regression': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c:174: warning: unused variable 'niter' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_matrix.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 8 [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_arpack.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_arpack.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_arpack.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/vmdio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c: In function 'load_vmd_library': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c:234: warning: unused variable 'filename' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/vmdio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/names.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/names.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/names.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrjac.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrjac.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrjac.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/confio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/confio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/do_fit.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/do_fit.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: In function 'read_espresso_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:451: warning: unused variable 'npar' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:451: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: In function 'read_stx_conf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:1397: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:1392: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/confio.c:880: warning: 'get_conf' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: In function 'calc_fit_R': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c:104: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: In function 'do_fit_ndim': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c:215: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/do_fit.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 10%] Building C object src/gmxlib/CMakeFiles/gmx.dir/typedefs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/typedefs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_block': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:108: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_blocka': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:118: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_atom': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:131: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:183: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: In function 'init_state': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c:533: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/typedefs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 9 [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/symtab.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/symtab.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/symtab.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mvdata.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mvdata.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sparsematrix.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/sparsematrix.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/sparsematrix.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_atoms': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:169: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_groups': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:187: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:327: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_ffparams': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:349: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_inputrec': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:466: warning: unused variable 'bAlloc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: In function 'bc_molblock': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:497: warning: unused variable 'bAlloc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mvdata.c:312: warning: 'bc_idef' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gbutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gbutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gbutil.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mshift.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mshift.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/md5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/md5.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: In function 'compact_graph': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c:249: warning: unused variable 'e' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: In function 'done_graph': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c:405: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mshift.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 12%] Building C object src/gmxlib/CMakeFiles/gmx.dir/futil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/futil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c: In function 'ffopen': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c:446: warning: unused variable 'bf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/futil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 10 [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/tcontrol.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/tcontrol.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/tcontrol.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/ewald_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/ewald_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/ewald_util.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/smalloc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/smalloc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c: In function 'save_free_aligned': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c:356: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/smalloc.c:356: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/oenv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/oenv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/oenv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 13%] /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/3dview.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/3dview.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_sort.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_sort.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_sort.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c: In function 'reset_view': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c:281: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/3dview.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/mtop_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_atomnr_to_molblock_ind': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:150: warning: unused variable 'atoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_atominfo_global': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:177: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_ilistloop_all_next': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:449: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gmx_mtop_global_cgs': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:503: warning: unused variable 'atoms' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c: In function 'gen_local_top': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:773: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/mtop_util.c:773: warning: unused variable 'ftype_dest' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 13%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nrama.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nrama.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 11 [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/wgms.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/wgms.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/wgms.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: In function 'get_dih2': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:182: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: In function 'init_rama': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:312: warning: unused variable 'ePBC' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nrama.c:179: warning: 'get_dih2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/rbin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/rbin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/rbin.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/chargegroup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/chargegroup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/chargegroup.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/network.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/network.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/invblock.c.o /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/invblock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/invblock.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: In function 'gmx_setup': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:82: warning: unused variable 'flag' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:82: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c:80: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/network.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xdrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/xdrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/xdrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/disre.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/disre.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 12 [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_rw.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_rw.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_rw.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 16%] [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_bin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmxfio_bin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio_bin.c Building C object src/gmxlib/CMakeFiles/gmx.dir/cinvsqrtdata.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/cinvsqrtdata.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/cinvsqrtdata.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: In function 'calc_disres_R_6': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'jt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:249: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'kj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'ki' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:244: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: In function 'ta_disres': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:372: warning: unused variable 'jt' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c:372: warning: unused variable 'it' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/disre.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/copyrite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/copyrite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: In function 'cool_quote': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c:193: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: In function 'please_cite': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c:535: warning: unused variable 'j' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/copyrite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_random.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_random.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 16%] [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selvalue.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selvalue.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selvalue.c Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_permute.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c: In function 'gmx_rng_update': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c:217: warning: unused variable 'lastx' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_random.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: In function 'init_output_permute': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c:192: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: In function 'evaluate_permute': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c:240: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_permute.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 13 [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_same.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 17%] [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selelem.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selhelp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selhelp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selhelp.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selelem.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selelem.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c: In function 'evaluate_same_str': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_same.c:499: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/scanner.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/scanner.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/scanner.c scanner.c:1396: warning: 'yyunput' defined but not used scanner.c:1438: warning: 'input' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/parsetree.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/parsetree.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_insolidangle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_insolidangle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_selelem_set_method': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:556: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_sel_init_comparison': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:652: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c: In function '_gmx_sel_init_modifier': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parsetree.c:835: warning: unused variable 'i' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/scanner_internal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/scanner_internal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/scanner_internal.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: In function 'evaluate_insolidangle': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:476: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: In function 'store_surface_point': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:829: warning: unused variable 'bin' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:829: warning: unused variable 'pbin' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_insolidangle.c:213: warning: 'set_comg_insolidangle' declared 'static' but never defined /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 14 [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/symrec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/parser.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/parser.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/parser.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c: In function 'add_symbol': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/symrec.c:395: warning: unused variable 'len' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/compiler.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/compiler.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_distance.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_distance.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_distance.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/mempool.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/mempool.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/mempool.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c: In function 'analyze_static': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c:2004: warning: unused variable 'next' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c:2004: warning: unused variable 'child' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/compiler.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/params.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/params.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_compare.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_compare.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_compare.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c: In function 'parse_values_varnum_expr': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c:676: warning: unused variable 'expr' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/params.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 15 [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_position.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_position.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_keywords.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_keywords.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_keywords.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selection.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selection.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selection.c /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_simple.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_simple.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/selmethod.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/selmethod.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/selmethod.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/evaluate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/evaluate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/evaluate.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_merge.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/selection/sm_merge.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/trajana.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c: In function 'init_merge': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c:182: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/selection/sm_merge.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: In function 'gmx_ana_traj_free': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c:322: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: In function 'gmx_ana_init_selections': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c:1200: warning: unused variable 'bOk' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/trajana.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 16 [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/position.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/position.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 21%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/poscalc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 21%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: In function 'merge_to_base': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c:797: warning: unused variable 'j' Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/nbsearch.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/nbsearch.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: In function 'gmx_ana_poscalc_update': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c:1282: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/poscalc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/displacement.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/displacement.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/indexutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/indexutil.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/trajana/centerofmass.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 21%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 17 [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/statistics/histogram.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/histogram.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c: In function 'gmx_calc_cog': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c:55: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/trajana/centerofmass.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: In function 'gmx_stats_dump_xy': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c:449: warning: unused variable 'ok' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c: In function 'gmx_stats_make_histogram': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/statistics/gmx_statistics.c:505: warning: unused variable 'ok' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_generic_cg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_generic_cg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nonbonded.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nonbonded.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c: In function 'gmx_nb_generic_cg_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:83: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:62: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c:61: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic_cg.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_free_energy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_free_energy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: In function 'do_nonbonded': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:313: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:311: warning: unused variable 'bWater' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:309: warning: unused variable 'sz' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: In function 'do_listed_vdw_q': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:664: warning: unused variable 'tmplist' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c:655: warning: unused variable 'i2' [ 23%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nonbonded.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_generic.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_generic.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c: In function 'gmx_nb_free_energy_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:102: warning: unused variable 'H' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:102: warning: unused variable 'G' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:91: warning: unused variable 'rinvsix' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c:88: warning: unused variable 'vcoul' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_free_energy.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel230.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel230.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c: In function 'gmx_nb_generic_kernel': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:81: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:61: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c:60: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_generic.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: In function 'nb_kernel230': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: In function 'nb_kernel230nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c:336: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel230.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 23%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel213.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel213.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 18 [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel312.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel312.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: In function 'nb_kernel213': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: In function 'nb_kernel213nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c:424: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel213.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel101.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel101.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: In function 'nb_kernel312': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: In function 'nb_kernel312nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c:733: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel312.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 24%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: In function 'nb_kernel101': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: In function 'nb_kernel101nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c:368: warning: unused variable 'gbtabscale'Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel223.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel223.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel101.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: In function 'nb_kernel223': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: In function 'nb_kernel223nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c:427: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel223.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel334.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel334.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 24%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: In function 'nb_kernel334': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c:84: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel210.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel210.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: In function 'nb_kernel334nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c:798: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel334.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: In function 'nb_kernel210': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: In function 'nb_kernel210nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c:304: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel210.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel112.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel112.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: In function 'nb_kernel112': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: In function 'nb_kernel112nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c:574: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel112.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 24%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 19 [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel130.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel130.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In function 'nb_kernel200': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In function 'nb_kernel200nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:286: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: In function 'nb_kernel130': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: In function 'nb_kernel130nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c:334: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel130.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel211.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel211.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel214.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel214.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: In function 'nb_kernel211': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: In function 'nb_kernel211nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c:390: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel211.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: In function 'nb_kernel214': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: In function 'nb_kernel214nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c:622: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel214.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c: In function 'setup_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c:113: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel110.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel110.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: In function 'nb_kernel110': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: In function 'nb_kernel110nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c:302: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel110.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel131.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel131.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 26%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel232.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel232.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 20 [ 27%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: In function 'nb_kernel131': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c:84: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel303.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel303.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: In function 'nb_kernel131nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c:418: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel131.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: In function 'nb_kernel232': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: In function 'nb_kernel232nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c:616: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel232.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: In function 'nb_kernel303': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: In function 'nb_kernel303nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel303.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel304.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel304.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel124.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel124.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: In function 'nb_kernel304': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: In function 'nb_kernel304nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c:715: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel304.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 27%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: In function 'nb_kernel124': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: In function 'nb_kernel124nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c:615: warning: unused variable 'gbtabscale' Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel430.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel430.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel124.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c: In function 'nb_kernel430': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c:105: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel430.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel221.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel221.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel420.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel420.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: In function 'nb_kernel221': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: In function 'nb_kernel221nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c:392: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel221.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c: In function 'nb_kernel420': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c:105: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel420.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel400.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel400.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 27%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel100.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel100.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c: In function 'nb_kernel400': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c:100: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel400.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 21 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 28%] [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel030.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel030.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel132.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel132.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: In function 'nb_kernel100': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: In function 'nb_kernel100nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c:284: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel100.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: In function 'nb_kernel132': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: In function 'nb_kernel132nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c:606: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: In function 'nb_kernel030':/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel132.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: In function 'nb_kernel030nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c:322: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel030.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel302.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel302.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel233.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel233.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: In function 'nb_kernel302': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: In function 'nb_kernel302nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c:715: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel302.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: In function 'nb_kernel233': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: In function 'nb_kernel233nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c:456: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel233.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel320.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel320.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: In function 'nb_kernel320': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: In function 'nb_kernel320nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c:327: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel320.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 28%] [ 28%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel123.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel123.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel204.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel204.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 22 [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: In function 'nb_kernel123': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: In function 'nb_kernel123nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel123.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: In function 'nb_kernel204': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: In function 'nb_kernel204nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c:568: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel204.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c: In function 'setup_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c:114: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel313.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel313.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel314.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel314.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: In function 'nb_kernel313': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: In function 'nb_kernel313nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c:476: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel313.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel333.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel333.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: In function 'nb_kernel314': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: In function 'nb_kernel314nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c:770: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel314.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: In function 'nb_kernel333': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: In function 'nb_kernel333nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c:504: warning: unused variable 'gbtabscale' [ 30%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel333.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel311.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel311.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: In function 'nb_kernel311': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: In function 'nb_kernel311nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c:443: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel311.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel331.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel331.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: In function 'nb_kernel331': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: In function 'nb_kernel331nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c:460: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel331.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 30%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel113.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel113.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 23 [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel121.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel121.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: In function 'nb_kernel113': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: In function 'nb_kernel113nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c:420: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel113.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 31%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: In function 'nb_kernel121':Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel010.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel010.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: In function 'nb_kernel121nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c:388: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel121.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel201.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel201.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: In function 'nb_kernel010': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c:85: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: In function 'nb_kernel010nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c:292: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel010.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: In function 'nb_kernel201': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: In function 'nb_kernel201nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c:372: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel201.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 31%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel330.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel330.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel102.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel102.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 31%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel020.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel020.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: In function 'nb_kernel330': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: In function 'nb_kernel330nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c:342: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: In function 'nb_kernel102': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel330.c: At top level:/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: In function 'nb_kernel102nf': /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c:558: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel102.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: In function 'nb_kernel020': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c:84: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 31%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: In function 'nb_kernel020nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c:294: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel020.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel231.c.o /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel231.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 24 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: In function 'nb_kernel231': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c:84: warning: unused variable 'gbtabscale' [ 32%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: In function 'nb_kernel231nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c:422: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel231.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel203.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel203.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel133.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel133.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: In function 'nb_kernel203': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: In function 'nb_kernel203nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c:372: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel203.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: In function 'nb_kernel133': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: In function 'nb_kernel133nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c:452: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel133.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel224.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel224.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel323.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel323.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel103.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel103.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: In function 'nb_kernel224': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: In function 'nb_kernel224nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c:625: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel224.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: In function 'nb_kernel323': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: In function 'nb_kernel323nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c:479: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel323.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: In function 'nb_kernel103': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: In function 'nb_kernel103nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c:368: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel103.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel322.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel322.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: In function 'nb_kernel322': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: In function 'nb_kernel322nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c:735: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel322.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 32%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel104.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel104.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: In function 'nb_kernel104': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: In function 'nb_kernel104nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c:558: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 25 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel104.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel324.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel324.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: In function 'nb_kernel324': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: In function 'nb_kernel324nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c:773: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel324.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel410.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel410.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c: In function 'nb_kernel410': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c:106: warning: unused variable 'fgb' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel410.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel202.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel202.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 34%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel212.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel212.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel114.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel114.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: In function 'nb_kernel202': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: In function 'nb_kernel202nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c:568: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel202.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: In function 'nb_kernel212': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: In function 'nb_kernel212nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c:584: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel212.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: In function 'nb_kernel114': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: In function 'nb_kernel114nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c:612: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel114.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel222.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel222.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: In function 'nb_kernel222': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: In function 'nb_kernel222nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c:586: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel222.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel332.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel332.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 34%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel300.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel300.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: In function 'nb_kernel332': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: In function 'nb_kernel332nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c:750: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel332.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 26 [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_c.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel_c.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: In function 'nb_kernel300': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: In function 'nb_kernel300nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c:305: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel300.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel301.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel301.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel134.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel134.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel321.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel321.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: In function 'nb_kernel301': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: In function 'nb_kernel301nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c:423: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel301.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: In function 'nb_kernel134': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: In function 'nb_kernel134nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c:644: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: In function 'nb_kernel321': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: In function 'nb_kernel321nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c:445: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel134.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel321.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel234.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel234.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 35%] [ 35%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel310.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel310.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel122.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel122.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: In function 'nb_kernel234': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: In function 'nb_kernel234nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c:654: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel234.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: In function 'nb_kernel310': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: In function 'nb_kernel310nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c:325: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel310.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: In function 'nb_kernel122': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: In function 'nb_kernel122nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c:576: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel122.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 27 [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel111.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel111.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: In function 'nb_kernel111': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: In function 'nb_kernel111nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c:386: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel111.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel120.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel120.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: In function 'nb_kernel120': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c:84: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: In function 'nb_kernel120nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c:304: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel120.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel220.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel220.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sger.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sger.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sger.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 36%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/srot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/srot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/srot.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: In function 'nb_kernel220': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c:84: warning: unused variable 'gbtabscale' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: In function 'nb_kernel220nf': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c:306: warning: unused variable 'gbtabscale' /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel220.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used [ 36%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dswap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dswap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dswap.c [ 36%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 28 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sgemm.c.o [ 38%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sgemm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sgemm.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dasum.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dasum.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dasum.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/daxpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/daxpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/daxpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/idamax.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/idamax.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/idamax.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 38%] [ 38%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dger.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dger.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dger.c [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dscal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dscal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dscal.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 38%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrsm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrsm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrsm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 29 [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ddot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ddot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ddot.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ssyr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/ssyr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssyr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sscal.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sscal.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sscal.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsyr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsyr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsyr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/isamax.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/isamax.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/isamax.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 39%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 39%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dgemv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dgemv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dgemv.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsyr2k.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsyr2k.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsyr2k.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 30 [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dgemm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dgemm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dgemm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrmv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrmv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrmv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dtrmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dtrmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dtrmm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 41%] [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dcopy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dcopy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dcopy.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sasum.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sasum.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sasum.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sgemv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sgemv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sgemv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 41%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dsymv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dsymv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dsymv.c [ 41%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/scopy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/scopy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/scopy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 31 [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/saxpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/saxpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/saxpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 42%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sswap.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sswap.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sswap.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 42%] [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/drot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/drot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/drot.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/sdot.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/sdot.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/sdot.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/dnrm2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/dnrm2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/dnrm2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 42%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 42%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/ssymv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include 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/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/ssyr2k.c [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strmv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/strmv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/strmv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/snrm2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_blas/snrm2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_blas/snrm2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_blas/strsm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && 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-DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstein.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstein.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 43%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlascl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlascl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlascl.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 33 [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlagtf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlagtf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlagtf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 45%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasdq.c.o [ 45%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasdq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasdq.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarf.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarnv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarnv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarnv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasv2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasv2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasv2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 45%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 34 [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slagts.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slagts.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slagts.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarft.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarft.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 46%] [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrbx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrbx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrbx.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstevr.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstevr.c [ 46%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaruv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaruv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaruv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 35 [ 46%] [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgeqrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgeqrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgeqrf.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormlq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormlq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormlq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorg2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorg2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorg2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasrt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasrt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasrt.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorgqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlamrg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlamrg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlamrg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 47%] [ 47%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd8.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd8.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd8.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slange.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slange.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slange.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 47%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 36 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormql.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormql.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormql.c [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd3.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetri.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetri.c [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasrt2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaswp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaswp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaswp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 49%] [ 49%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorm2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorm2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorm2r.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorglq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorglq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorglq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 37 [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorm2l.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorm2l.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorm2l.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 50%] [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd0.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd0.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd0.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd7.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd7.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd7.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorglq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorglq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorglq.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 50%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaruv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaruv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaruv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 50%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 38 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaev2.c.o [ 52%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaev2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaev2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd0.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd0.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd0.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 52%] [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slabrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slabrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slabrd.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sbdsqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sbdsqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slar1vx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slar1vx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slar1vx.c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsqr.c: In function 'sbdsqr_': /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsqr.c:61: warning: unused variable 'ftmp' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorgl2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorgl2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorgl2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstegr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstegr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstegr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 52%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 39 [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlacpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlacpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlacpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsterf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsterf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsterf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormtr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormtr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormtr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormql.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormql.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormql.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetf2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetf2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetf2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 53%] [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgebd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgebd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgebd2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasda.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasda.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasda.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 40 [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgebrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgebrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgebrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsteqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsteqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsteqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsyevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsyevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsyevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasdt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasdt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasdt.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 54%] [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstegr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstegr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstegr.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstein.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstein.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstein.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 54%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slacpy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slacpy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slacpy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 41 [ 56%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssytd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssytd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssytd2.c [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrvx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrvx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrvx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlas2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlas2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlas2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrbx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrbx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrbx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasv2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasv2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasv2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 42 [ 56%] [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaed6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaed6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaed6.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slartg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slartg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slartg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd4.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorgbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 57%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorml2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorml2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorml2.c [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssterf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssterf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssterf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorgbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorgbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorgbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 57%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarnv.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarnv.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarnv.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 43 [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ilasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ilasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ilasrt2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorgl2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorgl2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorgl2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 58%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 58%] [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorgqr.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgesdd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgesdd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgesdd.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorgqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorgqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaset.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaset.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaset.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 58%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasrt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasrt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasrt.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 44 [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq4.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlae2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlae2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlae2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 60%] [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sbdsdc.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsytrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsytrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsytrd.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sbdsdc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sbdsdc.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 60%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 60%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dtrtri.c.o [ 60%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dtrtri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dtrtri.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 45 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sstebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sstebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sstebz.c [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaswp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaswp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaswp.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 61%] [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarfg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarfg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarfg.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaev2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaev2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaev2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 61%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq2.c.o [ 61%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slascl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slascl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slascl.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slapy2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slapy2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slapy2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 61%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dtrti2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dtrti2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dtrti2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 61%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 46 [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slassq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slassq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slassq.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sormbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sormbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sormbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 63%] [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetf2.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasq4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasq4.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetf2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetf2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrex.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd7.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd7.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd7.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaed6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaed6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaed6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 47 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 64%] [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssytrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssytrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssytrd.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgelq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgelq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgelq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorm2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorm2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorm2r.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 64%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlansy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlansy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlansy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 48 [ 64%] [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasdq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasdq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasdq.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlanst.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlanst.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlanst.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dsytd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dsytd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dsytd2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd8.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd8.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd8.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlatrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlatrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlatrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetri.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetri.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 65%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 49 Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarfb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarfb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarfb.c [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssteqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssteqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssteqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slatrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slatrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slatrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorml2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorml2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorml2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlabrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlabrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlabrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgeqr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgeqr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgeqr2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 67%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 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-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 50 [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasda.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasda.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasda.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlaset.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlaset.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlaset.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slamrg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slamrg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slamrg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/strti2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/strti2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/strti2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgeqrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgeqrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgeqrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 68%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlartg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlartg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlartg.c [ 68%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dbdsqr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dbdsqr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 51 [ 69%] /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c: In function 'dbdsqr_':Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd2.c.o /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsqr.c:61: warning: unused variable 'ftmp' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 69%] [ 69%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgebd2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgebd2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgebd2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slaebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slaebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slaebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 69%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasdt.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasdt.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasdt.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 69%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarrfx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarrfx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarrfx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 69%] [ 69%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlange.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlange.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlange.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgelq2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgelq2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgelq2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 52 [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarfb.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarfb.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarfb.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/ssyevr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/ssyevr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/ssyevr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dstebz.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dstebz.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dstebz.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 71%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasrt2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasrt2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasrt2.c [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlar1vx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlar1vx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlar1vx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 71%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slagtf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slagtf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slagtf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 53 [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slas2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slas2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slas2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slansy.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slansy.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slansy.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd3.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 72%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarf.c [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd1.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd1.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd1.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 72%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sorg2r.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sorg2r.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sorg2r.c [ 72%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetrs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetrs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetrs.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 54 [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlapy2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlapy2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlapy2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 73%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dbdsdc.c.o [ 73%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dbdsdc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dbdsdc.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd4.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd4.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd4.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq5.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq5.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq5.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/strtri.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/strtri.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/strtri.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/sgetrf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/sgetrf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/sgetrf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 73%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasd6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasd6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasd6.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 55 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 75%] [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormlq.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormlq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormlq.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgesdd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgesdd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgesdd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 75%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlasq3.c.o [ 75%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlasq3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlasq3.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrvx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrvx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrvx.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 75%] [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgetrs.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slarrfx.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slarrfx.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slarrfx.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgetrs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgetrs.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 75%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlassq.c.o /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 56 cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlassq.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlassq.c [ 75%] [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasd6.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slae2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slasd6.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slasd6.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/slae2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/slae2.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dorm2l.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dorm2l.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dorm2l.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlarfg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormbr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgebrd.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 76%] [ 76%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dlagts.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dlagts.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dlagts.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dormtr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 57 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 78%] [ 78%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include 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/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 78%] [ 78%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgeqr2.c Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/lib64/openmpi/bin/mpicc -Dgmx_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -I/builddir/build/BUILD/gromacs-4.5.5/src/gmxlib -o CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmx_lapack/dgelqf.c Linking C shared library libgmx_openmpi_d.so cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicc -fPIC -O2 -g -pipe -Wall 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CMakeFiles/gmx.dir/gmx_lapack/dlasd6.c.o CMakeFiles/gmx.dir/gmx_lapack/dormlq.c.o CMakeFiles/gmx.dir/gmx_lapack/dgesdd.c.o CMakeFiles/gmx.dir/gmx_lapack/dlasq3.c.o CMakeFiles/gmx.dir/gmx_lapack/slarrvx.c.o CMakeFiles/gmx.dir/gmx_lapack/slarrfx.c.o CMakeFiles/gmx.dir/gmx_lapack/dgetrs.c.o CMakeFiles/gmx.dir/gmx_lapack/dlassq.c.o CMakeFiles/gmx.dir/gmx_lapack/slae2.c.o CMakeFiles/gmx.dir/gmx_lapack/slasd6.c.o CMakeFiles/gmx.dir/gmx_lapack/dorm2l.c.o CMakeFiles/gmx.dir/gmx_lapack/dlarfg.c.o CMakeFiles/gmx.dir/gmx_lapack/dormbr.c.o CMakeFiles/gmx.dir/gmx_lapack/dgebrd.c.o CMakeFiles/gmx.dir/gmx_lapack/dlagts.c.o CMakeFiles/gmx.dir/gmx_lapack/dormtr.c.o CMakeFiles/gmx.dir/gmx_lapack/slasq6.c.o CMakeFiles/gmx.dir/gmx_lapack/slanst.c.o CMakeFiles/gmx.dir/gmx_lapack/dgeqr2.c.o CMakeFiles/gmx.dir/gmx_lapack/dgelqf.c.o -ldl -lm cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/gmxlib && /usr/bin/cmake -E cmake_symlink_library libgmx_openmpi_d.so.6 libgmx_openmpi_d.so.6 libgmx_openmpi_d.so make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 [ 78%] Built target gmx make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/depend make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/openmpi-double /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib/CMakeFiles/md.dir/depend.internal". Scanning dependencies of target md make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/build make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 78%] [ 78%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 58 Building C object src/mdlib/CMakeFiles/md.dir/mdatom.c.o Building C object src/mdlib/CMakeFiles/md.dir/sim_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/sim_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdatom.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c [ 79%] [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall_sse2_single.c Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_mkl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_mkl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_mkl.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdebin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c: In function 'init_mdatoms': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:55: warning: unused variable 'ilist' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'nmol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdatom.c:50: warning: unused variable 'mb' /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'calc_virial': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:362: warning: unused variable 'virtest' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:361: warning: unused variable 'j' [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/coupling.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/coupling.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'finish_run': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1358: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: In function 'init_md': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1467: warning: unused variable 'mod' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1467: warning: unused variable 'tmpt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1466: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c:1466: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/sim_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'init_mdebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:544: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:136: warning: unused variable 'nh' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'upd_mdebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:650: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: In function 'print_ebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:929: warning: unused variable 'enxlambda_data' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:918: warning: unused variable 'nor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c:918: warning: unused variable 'ndr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'NHC_trotter': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:62: warning: unused variable 'jmax' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'boxv_trotter': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:184: warning: unused variable 'Winvm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:183: warning: unused variable 'T' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'n'[ 79%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:182: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'berendsen_pcoupl':Building C object src/mdlib/CMakeFiles/md.dir/qm_orca.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_orca.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:446: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'trotter_update': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:660: warning: unused variable 'consk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:657: warning: unused variable 'dumvir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:657: warning: unused variable 'dumpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'nd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'kT' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'reft' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'qmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:656: warning: unused variable 'bmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'dvdlcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'pcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:655: warning: unused variable 'ecorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:651: warning: unused variable 'ntgrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:651: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'init_npt_vars': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:784: warning: unused variable 'dumvir' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:784: warning: unused variable 'dumpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:783: warning: unused variable 'dt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'dvdlcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'pcorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:782: warning: unused variable 'ecorr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:780: warning: unused variable 'tcstat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:779: warning: unused variable 'gc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:779: warning: unused variable 'ntgrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: In function 'NPT_energy': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'Q' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'W' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:1001: warning: unused variable 'dbaro' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:998: warning: unused variable 'tau' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:998: warning: unused variable 'eta' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'ngtcall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'qmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c:997: warning: unused variable 'bmass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/coupling.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c: In function 'read_orca_output': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c:261: warning: unused variable 'atnum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_orca.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftw3.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftw3.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw3.c /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/partdec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/partdec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 79%] Building C object src/mdlib/CMakeFiles/md.dir/iteratedconstraints.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/iteratedconstraints.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'gmx_tx': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:101: warning: unused variable 'status' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:100: warning: unused variable 'flag' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'init_partdec_constraint': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:508: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'init_partdec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:563: warning: unused variable 'nodeid' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'create_vsitelist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:769: warning: unused variable 'minidx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: In function 'setup_parallel_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:831: warning: unused variable 'recvbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:831: warning: unused variable 'sendbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/partdec.c:765: warning: 'create_vsitelist' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c: In function 'done_iterating': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c:103: warning: unused variable 'xmin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/iteratedconstraints.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 59 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 80%] [ 80%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_double.c.o Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftw2.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftw2.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftw2.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_sse2_double.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_sse2_double.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 80%] Building C object src/mdlib/CMakeFiles/md.dir/vsite.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/vsite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 80%] [ 80%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'constr_vsiten': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:376: warning: unused variable 'xs' Building C object src/mdlib/CMakeFiles/md.dir/qmmm.c.o Building C object src/mdlib/CMakeFiles/md.dir/rf_util.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/rf_util.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'construct_vsites': cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qmmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'rtmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'vtmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:423: warning: unused variable 'reftmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:417: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite2': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:588: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite3FD': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:703: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:700: warning: unused variable 'fx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'spread_vsite_f': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1188: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'count_intercg_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1344: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'get_vsite_pbc': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1383: warning: unused variable 'cg_c' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: In function 'init_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c:1494: warning: unused variable 'cg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vsite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c: In function 'RF_excl_correction': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c:58: warning: unused variable 'top' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/rf_util.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c: In function 'update_QMMMrec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c:740: warning: unused variable 'MMatoms' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qmmm.c:140: warning: 'int_comp' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 80%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_box.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_box.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_box.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 80%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_parallel_3dfft.c.o /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c:46: warning: 'copy_int_array' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_parallel_3dfft.c:57: warning: 'make_slab2grid' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 60 [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/pppm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pppm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/shellfc.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/shellfc.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c: In function 'gmx_pppm_init': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:508: warning: unused variable 'spacing' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:508: warning: unused variable 'box_diag' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:507: warning: unused variable 'tol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:506: warning: unused variable 'rc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:506: warning: unused variable 'r1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:505: warning: unused variable 'grids' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'porder' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'nz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c:504: warning: unused variable 'nx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pppm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/minimize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/minimize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'predict_shells': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:118: warning: unused variable 'dt_3' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:118: warning: unused variable 'dt_2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'init_shell_flexcon': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:200: warning: unused variable 'mt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'init_adir': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:689: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:689: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:686: warning: unused variable 'scale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'gt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'ga' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:685: warning: unused variable 'gf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: In function 'relax_shell_flexcon': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:777: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:772: warning: unused variable 'xiS' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:772: warning: unused variable 'xiH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c:770: warning: unused variable 'dx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shellfc.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'get_f_norm_max': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:185: warning: unused variable 'fmax2_0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:909: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:895: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:894: warning: unused variable 'sfm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_lbfgs': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:1431: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_steep': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2059: warning: unused variable 'terminate' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2049: warning: unused variable 'dvdlambda' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2048: warning: unused variable 'constepsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: In function 'do_nm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2269: warning: unused variable 'fmax' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2269: warning: unused variable 'fnorm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:2255: warning: unused variable 'bNS' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:569: warning: 'do_x_step' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/minimize.c:591: warning: 'do_x_sub' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/shakef.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/shakef.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'cshake': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:112: warning: unused variable 'tjx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tiz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tiy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:111: warning: unused variable 'tix' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'vec_shakef': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'rvscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'rscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'vscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:193: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: In function 'crattle': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:461: warning: unused variable 'tjx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tiz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tiy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:460: warning: unused variable 'tix' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'jmdt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'imdt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'diff' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:458: warning: unused variable 'rijd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:456: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:454: warning: unused variable 'mytol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/shakef.c:83: warning: 'pv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/md_support.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/md_support.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c: In function 'compute_globals': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:297: warning: unused variable 'temp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:297: warning: unused variable 'ekin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:294: warning: unused variable 'bVV' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c:293: warning: unused variable 'shakeall_vir' [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/ebin.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ebin.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/md_support.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c: In function 'add_ebin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:127: warning: unused variable 'sigma' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:127: warning: unused variable 'sum' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ebin.c:54: warning: 'rms_ener' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 82%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall_sse2_double.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 82%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 61 Building C object src/mdlib/CMakeFiles/md.dir/vcm.c.o [ 83%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/vcm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c Building C object src/mdlib/CMakeFiles/md.dir/fft5d.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/fft5d.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/fft5d.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'calc_vcm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'zz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'yz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'yy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:121: warning: unused variable 'xx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'do_stopcm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:170: warning: unused variable 'tm_1'/builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/fft5d.c:115: warning: 'lpfactor' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:170: warning: unused variable 'tm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:169: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: In function 'check_cm_grp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c:249: warning: unused variable 'Tcm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/vcm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/constr.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/constr.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 83%] /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'too_many_constraint_warnings': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:185: warning: unused variable 'abort' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'constrain': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:306: warning: unused variable 'vstor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:304: warning: unused variable 'ncons' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:303: warning: unused variable 'd' Building C object src/mdlib/CMakeFiles/md.dir/perf_est.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/perf_est.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'init_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:955: warning: unused variable 'natoms' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: In function 'inter_charge_group_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:1120: warning: unused variable 'nat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/constr.c:163: warning: 'icomp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c: In function 'pme_load_estimate': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c:91: warning: unused variable 'fljtab' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/perf_est.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/nsgrid.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/nsgrid.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'set_grid_sizes': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:206: warning: unused variable 'stddev' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:206: warning: unused variable 'av' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'init_grid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:361: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:361: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: In function 'grid_first': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c:474: warning: unused variable 'cx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nsgrid.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/wnblist.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/wnblist.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: In function 'read_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'icmp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'full' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:137: warning: unused variable 'nnbl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:136: warning: unused variable 'b2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:136: warning: unused variable 'b1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:135: warning: unused variable 'bNL' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: In function 'dump_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c:234: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wnblist.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mvxvf.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mvxvf.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 83%] Building C object src/mdlib/CMakeFiles/md.dir/pme_pp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pme_pp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme_pp.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 62 [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ewald.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c: In function 'init_ewald_tab': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c:105: warning: unused variable 'n' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ewald.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/edsam.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/edsam.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/edsam.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/qm_gamess.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_gamess.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_gamess.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_xml.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_qhop_xml.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft_fftpack.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft_fftpack.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft_fftpack.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'qhop_process_attr': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:182: warning: unused variable 'eprop' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'qhop_process_tree': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:247: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'gmx_qhops_read': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:279: warning: unused variable 'npd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:279: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'add_xml_qhop': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:311: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:310: warning: unused variable 'comp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:310: warning: unused variable 'grandchild' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c: In function 'gmx_qhops_write': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_xml.c:333: warning: unused variable 'nmt' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/csettle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/csettle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 84%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_network.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_network.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_network.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'settle_proj': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:189: warning: unused variable 'kfacHH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:189: warning: unused variable 'kfacOH' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:188: warning: unused variable 'invvscale' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:187: warning: unused variable 'derpm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'xshake': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:305: warning: unused variable 'conv' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: In function 'csettle': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c:417: warning: unused variable 'shakeret' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/csettle.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 63 [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/wall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/wall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/genborn.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c: In function 'do_walls': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c:109: warning: unused variable 'Heps' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/wall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'init_gb_still': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'rbc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'rab' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'cosine' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'factor' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p3' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:206: warning: unused variable 'p1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:205: warning: unused variable 'rk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:205: warning: unused variable 'r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:204: warning: unused variable 'angle' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:204: warning: unused variable 'length' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:202: warning: unused variable 'ibm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:202: warning: unused variable 'iam' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'at' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'idx2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'id' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'ic' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nang' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'nbond' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'i2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:201: warning: unused variable 'i1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'init_gb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:390: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'ai' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:389: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_still': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:518: warning: unused variable 'dr4' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:518: warning: unused variable 'dr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:515: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_hct': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:656: warning: unused variable 'duij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:652: warning: unused variable 'gpi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:649: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:649: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad_obc': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:875: warning: unused variable 'duij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:872: warning: unused variable 'min_rad' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:872: warning: unused variable 'rad' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:871: warning: unused variable 'gpi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:868: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:868: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_rad': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1094: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'gb_bonds_tab': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1346: warning: unused variable 'dvdaj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1346: warning: unused variable 'vcoul' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1339: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_nonpolar': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1477: warning: unused variable 'rbi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_chainrule': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1550: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1548: warning: unused variable 'rinv11' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1547: warning: unused variable 'rsq11' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1546: warning: unused variable 'rb2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1546: warning: unused variable 'fij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'calc_gb_forces': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1663: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1661: warning: unused variable 'v' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: In function 'make_gb_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1887: warning: unused variable 'apa' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'found' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'at1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'at0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1886: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn.c:1875: warning: 'compare_int' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/forcerec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/forcerec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin_bar.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/mdebin_bar.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin_bar.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'check_solvent_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:164: warning: unused variable 'excl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'set_avcsixtwelve': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:769: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: In function 'init_forcerec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1299: warning: unused variable 'ngrp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1299: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/forcerec.c:1235: warning: 'forcerec_check_sse2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/mdebin_bar.c:99: warning: 'mde_delta_h_free' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/init.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/init.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c: In function 'set_state_entries': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c:73: warning: unused variable 'nnhpres' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/init.c:64: warning: 'int_title' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_con.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_con.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: In function 'dd_make_local_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c:950: warning: unused variable 'gat' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: In function 'init_domdec_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c:1074: warning: unused variable 'dc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_con.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 86%] Building C object src/mdlib/CMakeFiles/md.dir/nlistheuristics.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/nlistheuristics.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/nlistheuristics.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 64 [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/clincs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/clincs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/tgroup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tgroup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: In function 'do_lincsp': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'lam' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'wfac' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:191: warning: unused variable 'rlen' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: In function 'init_grptcstat': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c:56: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: In function 'constrain_lincs': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:1165: warning: unused variable 'error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: In function 'sum_ekin': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c:204: warning: unused variable 'ek' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tgroup.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/clincs.c:1114: warning: 'dump_conf' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/pull.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pull.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/calcvir.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: In function 'get_pullgrps_dr': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:301: warning: unused variable 'pref' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: In function 'do_constraint': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:458: warning: unused variable 'mass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c:457: warning: unused variable 'd0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pull.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_parm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_qhop_parm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_qhop_parm.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c:46: warning: 'dprod1' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcvir.c:159: warning: 'lo_fcv2' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/calcmu.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/calcmu.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/calcmu.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 87%] Building C object src/mdlib/CMakeFiles/md.dir/groupcoord.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/groupcoord.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/groupcoord.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 65 [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/stat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/stat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/stat.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_allvsall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: In function 'setup_gb_exclusions_and_indices': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:119: warning: unused variable 'nj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:116: warning: unused variable 'nj1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:116: warning: unused variable 'nj0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:114: warning: unused variable 'tp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: In function 'genborn_allvsall_setup': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:330: warning: unused variable 'p' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'idx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c:328: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_allvsall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/update.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/update.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'print_missing_interactions_mb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:114: warning: unused variable 'a_gl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:114: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'global_atomnr_to_moltype_ind': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:364: warning: unused variable 'molb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'count_excls': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:379: warning: unused variable 'n_inter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_make_reverse_top': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:628: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:628: warning: unused variable 'n_recursive_vsite' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'add_vsite': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:772: warning: unused variable 'iatoms_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'make_local_exclusions': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1234: warning: unused variable 'a_loc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_make_local_top': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1422: warning: unused variable 'bUniqueExcl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'dd_init_local_state': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1576: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1576: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: In function 'check_link': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c:1616: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'do_update_vv_vel': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vnrel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'va' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vv' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'vn' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:238: warning: unused variable 'u' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:237: warning: unused variable 'vrel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:236: warning: unused variable 'gt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:235: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'do_update_vv_pos': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:287: warning: unused variable 'w_dt' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:287: warning: unused variable 'imass' [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/domdec.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_tcouple': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'homenr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1155: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_constraints': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1303: warning: unused variable 'vbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1301: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1298: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1298: warning: unused variable 'bExtended' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_box': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1470: warning: unused variable 'vir_con' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1469: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1468: warning: unused variable 'dt_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bEner' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bLog' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bLastStep' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1466: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: In function 'update_coords': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xprimein' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xpall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'fall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'forcein' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vall' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'xcom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1588: warning: unused variable 'vcom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1587: warning: unused variable 'vir_con' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1586: warning: unused variable 'icom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nexpand' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nconstr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nsettle' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'nshake' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'jatom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'iatom' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'blen1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1585: warning: unused variable 'blen0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'g' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1584: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1581: warning: unused variable 'imassin' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1581: warning: unused variable 'imass' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bEner' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bLog' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bLastStep' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c:1579: warning: unused variable 'bTrotter' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/update.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/domdec_setup.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/domdec_setup.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_move_cellx': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:982: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:982: warning: unused variable 'dim1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_collect_vec': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1432: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'a' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1431: warning: unused variable 'n' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1430: warning: unused variable 'ma' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_distribute_vec_scatterv': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1667: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_distribute_state': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1709: warning: unused variable 'ngtcp' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:1709: warning: unused variable 'ngtch' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'gmx_ddcoord2pmeindex': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2075: warning: unused variable 'nc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2075: warning: unused variable 'coords_pme' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'make_dd_indices': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2393: warning: unused variable 'ga2la' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'check_bLocalCG': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:2449: warning: unused variable 'ncg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'set_dd_cell_sizes_dlb_root': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3183: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'distribute_dd_cell_sizes_dlb': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3365: warning: unused variable 'dim1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'distribute_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3657: warning: unused variable 'bUnbounded' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3653: warning: unused variable 'box_size' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:3651: warning: unused variable 'npbcdim' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_redistribute_cg': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4177: warning: unused variable 'cell_d' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4177: warning: unused variable 'd4' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'get_load_distribution': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:4849: warning: unused variable 'cid' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'setup_dd_grid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:5309: warning: unused variable 'bZYX' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'check_dlb_support': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6039: warning: unused variable 'dd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'init_domain_decomposition': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6181: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'guess_npme': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:145: warning: unused variable 'ir_try' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:144: warning: unused variable 'nky' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:144: warning: unused variable 'nkx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_init_bondeds': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6694: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:6693: warning: unused variable 'bBondComm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'comm_cost_est': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:298: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: In function 'assign_factors': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c:486: warning: unused variable 'z' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'setup_dd_communication': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'inv_ncg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r2inc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_1' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_scomm2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:7139: warning: unused variable 'r_mb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec_setup.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: In function 'dd_partition_system': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c:8178: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/domdec.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:291: warning: 'ga2la_get_home' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/ghat.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ghat.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ghat.c /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 89%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_fft.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_fft.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_fft.c /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 66 [ 90%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tables.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/pullutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pullutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'done_tabledata': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:483: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'make_tables': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:868: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: In function 'make_gb_table': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:991: warning: unused variable 'x0_r2_error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:991: warning: unused variable 'x0_r_error' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:990: warning: unused variable 'rel_error_r2_old' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:990: warning: unused variable 'rel_error_r_old' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:989: warning: unused variable 'rel_error_r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:989: warning: unused variable 'rel_error_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:988: warning: unused variable 'abs_error_r2' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:988: warning: unused variable 'abs_error_r' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'tabsel' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:982: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:977: warning: unused variable 'fns14' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tables.c:159: warning: 'splint' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: In function 'pull_set_pbcatom': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c:85: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: In function 'pull_calc_coms': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c:281: warning: unused variable 'xx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pullutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:90: warning: 'ga2la_init' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:133: warning: 'ga2la_set' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:182: warning: 'ga2la_del' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:226: warning: 'ga2la_change_la' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:259: warning: 'ga2la_get' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmx_ga2la.h:327: warning: 'ga2la_is_home' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/ns.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/ns.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'init_neighbor_list': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:248: warning: unused variable 'solvent' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'new_i_nblist': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'nshift' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:419: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'put_in_list_at': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:640: warning: unused variable 'rlj' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:640: warning: unused variable 'qq' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:635: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:633: warning: unused variable 'ind_ij' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_inner_tric': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1466: warning: unused variable 'nsbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_inner_rect': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1499: warning: unused variable 'nsbuf' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'ns_simple_core': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'i0' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1552: warning: unused variable 'jcg' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'nsgrid_core': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcy' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1950: warning: unused variable 'dcx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1949: warning: unused variable 'xi' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1945: warning: unused variable 'nri' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'init_ns': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2402: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: In function 'search_neighbours': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2528: warning: unused variable 'cg_end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2528: warning: unused variable 'cg_start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2527: warning: unused variable 'i_egp_flags' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2526: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2522: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:2522: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/ns.c:1637: warning: 'get_dx' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/qm_gaussian.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_gaussian.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_gaussian.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 90%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/tpi.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/tpi.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/qm_mopac.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/qm_mopac.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 90%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_wallcycle.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/gmx_wallcycle.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/gmx_wallcycle.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c: In function 'do_tpi': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:160: warning: unused variable 'dvdl' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:150: warning: unused variable 'end' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:150: warning: unused variable 'start' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c:135: warning: unused variable 'TPI' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/tpi.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 67 [ 91%] Building C object src/mdlib/CMakeFiles/md.dir/pme.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/pme.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'pmeredist_pd': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:399: warning: unused variable 'idxa' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'copy_pmegrid_to_fftgrid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:851: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'copy_fftgrid_to_pmegrid': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:917: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'spread_q_bsplines': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1105: warning: unused variable 'bndsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1105: warning: unused variable 'localsize' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1100: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1099: warning: unused variable 'ol' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'init_atomcomm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 's' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1807: warning: unused variable 'nk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'init_overlap_comm': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1854: warning: unused variable 'nk' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1854: warning: unused variable 'nn' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1853: warning: unused variable 'exten' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'maxlr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'rbnd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:1852: warning: unused variable 'lbnd' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'gmx_pme_init': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2039: warning: unused variable 'atc' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: In function 'gmx_pme_do': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2468: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2464: warning: unused variable 'local_ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'nz' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'ny' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2463: warning: unused variable 'nx' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/pme.c:2004: warning: 'gmx_pme_check_grid_restrictions' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 91%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_single.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/genborn_sse2_single.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/genborn_sse2_single.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 91%] Building C object src/mdlib/CMakeFiles/md.dir/force.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/lib64/openmpi/bin/mpicc -Dmd_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/md.dir/force.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: In function 'ns': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:86: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: In function 'do_force_lowlevel': /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:147: warning: unused variable 'dvdgb' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c:141: warning: unused variable 'bDoEpot' /builddir/build/BUILD/gromacs-4.5.5/src/mdlib/force.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Linking C shared library libmd_openmpi_d.so cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -shared -Wl,-soname,libmd_openmpi_d.so.6 -o libmd_openmpi_d.so.6 CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/iteratedconstraints.c.o CMakeFiles/md.dir/gmx_fft_fftw2.c.o CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/domdec_box.c.o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/pppm.c.o CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/minimize.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/constr.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/nsgrid.c.o CMakeFiles/md.dir/wnblist.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/ewald.c.o CMakeFiles/md.dir/edsam.c.o CMakeFiles/md.dir/qm_gamess.c.o CMakeFiles/md.dir/gmx_qhop_xml.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/wall.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/forcerec.c.o CMakeFiles/md.dir/mdebin_bar.c.o CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/calcvir.c.o CMakeFiles/md.dir/gmx_qhop_parm.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/update.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/ghat.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/pullutil.c.o CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/force.c.o ../gmxlib/libgmx_openmpi_d.so.6 -ldl -lm -lfftw3 -lxml2 cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/mdlib && /usr/bin/cmake -E cmake_symlink_library libmd_openmpi_d.so.6 libmd_openmpi_d.so.6 libmd_openmpi_d.so make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 58 59 60 61 62 63 64 65 66 67 [ 91%] Built target md make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/depend make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/openmpi-double /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel/CMakeFiles/gmxpreprocess.dir/depend.internal". Scanning dependencies of target gmxpreprocess make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/build make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 91%] [ 91%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 91%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/add_par.c.o Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/compute_io.c.o [ 91%] cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/compute_io.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/add_par.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/add_par.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/convparm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/convparm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gen_ad.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gen_ad.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c: In function 'compute_io': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/compute_io.c:61: warning: unused variable 'nfep' /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'assign_param': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:96: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'new_interaction_list': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:459: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: In function 'convert_params': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:469: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/convparm.c:457: warning: 'new_interaction_list' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 91%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'get_impropers': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:437: warning: unused variable 'r' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:436: warning: unused variable 'hbidih' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:434: warning: unused variable 'a0' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'clean_excls': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:576: warning: unused variable 'n' Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:576: warning: unused variable 'm' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: In function 'generate_excls': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'e' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'l1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'k1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:618: warning: unused variable 'j1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:114: warning: 'aeq' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:289: warning: 'ideq' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_ad.c:327: warning: 'dump_param' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'read_vsite_database': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:150: warning: unused variable 'prevdir' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:150: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'add_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:487: warning: unused variable 'bb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'gen_vsites_trp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:759: warning: unused variable 'c' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:758: warning: unused variable 'mtot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:758: warning: unused variable 'mwtot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:756: warning: unused variable 'xM' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:747: warning: unused variable 'dist' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:746: warning: unused variable 'I' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'gen_vsites_tyr': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:986: warning: unused variable 'vmass' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: In function 'do_vsites': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c:1350: warning: unused variable 'bb' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gen_vsite.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used[ 91%] /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/genhydro.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/genhydro.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'expand_hackblocks_one': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:161: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'check_atoms_present': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:275: warning: unused variable 'd' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 69 /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: In function 'add_h_low': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c:390: warning: unused variable 'd' [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genhydro.c: At top level: cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gpp_atomtype.c /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gpp_bond_atomtype.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/h_db.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/h_db.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 93%] [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/hackblock.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/hackblock.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hackblock.c Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/hizzie.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/hizzie.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: In function 'dump_h_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:117: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: In function 'read_h_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:200: warning: unused variable 'fp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/h_db.c:113: warning: 'dump_h_db' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c: In function 'set_histp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:195: warning: unused variable 'd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:192: warning: unused variable 'his0' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:192: warning: unused variable 'aj' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c:188: warning: unused variable 'bHaveH' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/hizzie.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/nm2type.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/nm2type.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: In function 'rd_nm2type_file': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c:72: warning: unused variable 'blen' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: In function 'nm2type': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c:179: warning: unused variable 'quality' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/nm2type.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 93%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/pdb2top.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/pdb2top.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 70 [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/pgutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/pgutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pgutil.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'missing_atoms': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:85: warning: unused variable 'bRet' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/readir.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/readir.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'print_top_comment': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:539: warning: unused variable 'tmp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'get_hackblocks_rtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:983: warning: unused variable 'bC' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:983: warning: unused variable 'bN' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:981: warning: unused variable 'Hnum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:980: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'match_atomnames_with_rtp_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1160: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'match_atomnames_with_rtp': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1324: warning: unused variable 'bFoundInAdd' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1323: warning: unused variable 'start_nr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1322: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1322: warning: unused variable 'start_at' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1321: warning: unused variable 'anmnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1320: warning: unused variable 'hbr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1317: warning: unused variable 'newnm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1316: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: In function 'gen_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1354: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:1354: warning: unused variable 'ii' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c:743: warning: 'inter_res_bond' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/readpull.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/readpull.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'check_ir': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:162: warning: unused variable 'ns_type' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'do_index': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:1782: warning: unused variable 'SAtime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: In function 'triple_check': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c:2293: warning: unused variable 'npct' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c: In function 'read_pullparams': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c:107: warning: unused variable 'dummy' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c:103: warning: unused variable 'nchar' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readpull.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/resall.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/resall.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/sorting.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/sorting.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/sorting.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c: In function 'read_resall': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c:256: warning: unused variable 'ptr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/resall.c:482: warning: 'neq_str' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/specbond.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/specbond.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/specbond.c /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/ter_db.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/ter_db.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'read_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:84: warning: unused variable 'type' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'print_ter_db': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:136: warning: unused variable 'nname' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: In function 'filter_ter': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:375: warning: unused variable 's2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c:373: warning: unused variable 'len' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ter_db.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 94%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/tomorse.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/tomorse.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tomorse.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 71 [ 95%] /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topdirs.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topdirs.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topdirs.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topexcl.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topexcl.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 95%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c: In function 'generate_excl': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c:356: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topexcl.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topio.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/toppush.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/toppush.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: In function 'generate_gb_exclusion_interactions': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n14' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_nbt': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:794: warning: unused variable 'sig6' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:792: warning: unused variable 'atnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:787: warning: unused variable 'form2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n13' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:390: warning: unused variable 'n12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:389: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:389: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_cmaptype': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:920: warning: unused variable 'bAllowRepeat' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:915: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: In function 'read_topol': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c:517: warning: unused variable 'block' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'default_cmap_params': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1312: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_bond': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1485: warning: unused variable 'paramB' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: In function 'push_cmap': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'param_defB' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'param_defA' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c:1799: warning: unused variable 'paramB' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topio.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/topshake.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/topshake.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c: In function 'make_shake': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c:98: warning: unused variable 'b' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c:98: warning: unused variable 'nb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/topshake.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/toputil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/toputil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toputil.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toputil.c:175: warning: 'print_nbt' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 95%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_block': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:298: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_blocka': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'k' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:308: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_atom': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:321: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:320: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_top': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'cmp_groups': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:376: warning: unused variable 'ndiff' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'comp_tpx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:715: warning: unused variable 'sh' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: In function 'comp_enx': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:1048: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c:1045: warning: unused variable 'block' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/tpbcmp.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 72 [ 97%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_bonds': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'vsitetype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:885: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_angles': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'vsitetype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1058: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: In function 'clean_vsite_dihs': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'l' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'parnr' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c:1153: warning: unused variable 'ftype' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/vsite_parm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 97%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/fflibutil.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/fflibutil.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c: In function 'low_fflib_search_file_end': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:159: warning: unused variable 'pdum' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:153: warning: unused variable 'buf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c:151: warning: unused variable 'ret' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/src/kernel/fflibutil.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used [ 97%] Building C object src/kernel/CMakeFiles/gmxpreprocess.dir/xlate.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -Dgmxpreprocess_EXPORTS -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/gmxpreprocess.dir/xlate.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xlate.c /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used Linking C shared library libgmxpreprocess_openmpi_d.so cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicc -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -shared -Wl,-soname,libgmxpreprocess_openmpi_d.so.6 -o libgmxpreprocess_openmpi_d.so.6 CMakeFiles/gmxpreprocess.dir/add_par.c.o CMakeFiles/gmxpreprocess.dir/compute_io.c.o CMakeFiles/gmxpreprocess.dir/convparm.c.o CMakeFiles/gmxpreprocess.dir/gen_ad.c.o CMakeFiles/gmxpreprocess.dir/gen_vsite.c.o CMakeFiles/gmxpreprocess.dir/genhydro.c.o CMakeFiles/gmxpreprocess.dir/gpp_atomtype.c.o CMakeFiles/gmxpreprocess.dir/gpp_bond_atomtype.c.o CMakeFiles/gmxpreprocess.dir/h_db.c.o CMakeFiles/gmxpreprocess.dir/hackblock.c.o CMakeFiles/gmxpreprocess.dir/hizzie.c.o CMakeFiles/gmxpreprocess.dir/nm2type.c.o CMakeFiles/gmxpreprocess.dir/pdb2top.c.o CMakeFiles/gmxpreprocess.dir/pgutil.c.o CMakeFiles/gmxpreprocess.dir/readir.c.o CMakeFiles/gmxpreprocess.dir/readpull.c.o CMakeFiles/gmxpreprocess.dir/resall.c.o CMakeFiles/gmxpreprocess.dir/sorting.c.o CMakeFiles/gmxpreprocess.dir/specbond.c.o CMakeFiles/gmxpreprocess.dir/ter_db.c.o CMakeFiles/gmxpreprocess.dir/tomorse.c.o CMakeFiles/gmxpreprocess.dir/topdirs.c.o CMakeFiles/gmxpreprocess.dir/topexcl.c.o CMakeFiles/gmxpreprocess.dir/topio.c.o CMakeFiles/gmxpreprocess.dir/toppush.c.o CMakeFiles/gmxpreprocess.dir/topshake.c.o CMakeFiles/gmxpreprocess.dir/toputil.c.o CMakeFiles/gmxpreprocess.dir/tpbcmp.c.o CMakeFiles/gmxpreprocess.dir/vsite_parm.c.o CMakeFiles/gmxpreprocess.dir/fflibutil.c.o CMakeFiles/gmxpreprocess.dir/xlate.c.o ../mdlib/libmd_openmpi_d.so.6 ../gmxlib/libgmx_openmpi_d.so.6 -ldl -lm -lfftw3 -lxml2 cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/bin/cmake -E cmake_symlink_library libgmxpreprocess_openmpi_d.so.6 libgmxpreprocess_openmpi_d.so.6 libgmxpreprocess_openmpi_d.so make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 69 70 71 72 [ 97%] Built target gmxpreprocess make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/depend make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/openmpi-double /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake --color= Dependee "/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel/CMakeFiles/mdrun.dir/depend.internal". Scanning dependencies of target mdrun make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/build make[3]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 97%] [ 97%] /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 73 /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/gctio.c.o Building C object src/kernel/CMakeFiles/mdrun.dir/ionize.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/ionize.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/ionize.c cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/gctio.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/gctio.c [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/runner.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/runner.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c Building C object src/kernel/CMakeFiles/mdrun.dir/do_gct.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/do_gct.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:46: warning: 'constraints' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/readir.h:52: warning: 'couple_lam' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c: In function 'mdrunner': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:368: warning: unused variable 'nthreads' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:367: warning: unused variable 'cr_old' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:362: warning: unused variable 'list' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:359: warning: unused variable 'gro' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'nalloc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'm' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:358: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:348: warning: unused variable 'tmpr2' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:348: warning: unused variable 'tmpr1' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:342: warning: unused variable 'realtime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c:342: warning: unused variable 'nodetime' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/runner.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: In function 'init_coupling': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:62: warning: unused variable 'atj' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:62: warning: unused variable 'ati' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'j' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'index' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'nc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:61: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: In function 'do_coupling': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:493: warning: unused variable 'bTest' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:491: warning: unused variable 'xi12' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:491: warning: unused variable 'xi6' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffc' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffb' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:490: warning: unused variable 'ffa' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:489: warning: unused variable 'rmsf' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/do_gct.c:461: warning: 'dump_fm' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/repl_ex.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/repl_ex.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: In function 'init_replica_exchange': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:118: warning: unused variable 'temp' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: In function 'replica_exchange': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:725: warning: unused variable 'shift' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/repl_ex.c:706: warning: 'write_debug_x' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/xutils.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/xutils.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/md.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/md.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c: In function 'update_forcefield': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c:334: warning: unused variable 'bDone' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/xutils.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c: In function 'do_md': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:184: warning: unused variable 'iter_i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:179: warning: unused variable 'oldfom' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:179: warning: unused variable 'fom' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:178: warning: unused variable 'tmpvir' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:174: warning: unused variable 'grpname' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:164: warning: unused variable 'timestep' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:140: warning: unused variable 'ebox' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c:140: warning: unused variable 'scale_tot' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/mdrun.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/mdrun.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/genalg.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/genalg.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 74 /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c: In function 'main': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:551: warning: unused variable 'i' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:503: warning: unused variable 'fptest' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:498: warning: unused variable 'ed' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:387: warning: unused variable 'bPPPME' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c:386: warning: unused variable 'bCart' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/mdrun.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used [100%] /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c: In function 'update_ga': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c:196: warning: unused variable 'j' Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/lib64/openmpi/bin/mpicc -DMPI -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -I/usr/include/libxml2 -I/builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src -I/builddir/build/BUILD/gromacs-4.5.5/include -o CMakeFiles/mdrun.dir/md_openmm.c.o -c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c /builddir/build/BUILD/gromacs-4.5.5/src/kernel/genalg.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c: In function 'do_md_openmm': /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c:151: warning: unused variable 'reset_counters_now' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c:151: warning: unused variable 'reset_counters' /builddir/build/BUILD/gromacs-4.5.5/src/kernel/md_openmm.c: At top level: /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:76: warning: 'sy_const' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:152: warning: 'gmx_numzero' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/maths.h:159: warning: 'gmx_log2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:819: warning: 'calc_lll' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:846: warning: 'm_rveccopy' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/vec.h:856: warning: 'matrix_convert' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/readinp.h:119: warning: 'argtp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:51: warning: 'pdbformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/pdbio.h:52: warning: 'pdbformat4' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/grompp.h:150: warning: 'ds' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/force.h:51: warning: 'sepdvdlformat' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:48: warning: 'cnul' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:60: warning: 'rcexp' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:71: warning: 'cadd' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:81: warning: 'csub' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:111: warning: 'cabs2' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/gmxcomplex.h:121: warning: 'cdiv' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:55: warning: 'CopyrightText' defined but not used /builddir/build/BUILD/gromacs-4.5.5/include/copyrite.h:69: warning: 'GPLText' defined but not used Linking C executable mdrun cd /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/src/kernel && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -Wa,--noexecstack -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc -O3 -DNDEBUG -fPIC CMakeFiles/mdrun.dir/gctio.c.o CMakeFiles/mdrun.dir/ionize.c.o CMakeFiles/mdrun.dir/runner.c.o CMakeFiles/mdrun.dir/do_gct.c.o CMakeFiles/mdrun.dir/repl_ex.c.o CMakeFiles/mdrun.dir/xutils.c.o CMakeFiles/mdrun.dir/md.c.o CMakeFiles/mdrun.dir/mdrun.c.o CMakeFiles/mdrun.dir/genalg.c.o CMakeFiles/mdrun.dir/md_openmm.c.o -o mdrun -rdynamic -ldl -lm libgmxpreprocess_openmpi_d.so.6 ../mdlib/libmd_openmpi_d.so.6 ../gmxlib/libgmx_openmpi_d.so.6 -ldl -lm -lfftw3 -lxml2 make[3]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 73 74 [100%] Built target mdrun make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/openmpi-double/CMakeFiles 0 make[1]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/openmpi-double' + cd .. + . /etc/profile.d/modules.sh ++++ /bin/ps -p 29018 -ocomm= +++ /bin/basename sh ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ MODULESHOME=/usr/share/Modules +++ export MODULESHOME +++ '[' openmpi-ppc64 = '' ']' +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module unload openmpi-ppc64 ++ /usr/bin/modulecmd sh unload openmpi-ppc64 + eval PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/bin ';export' 'PATH;unset' 'LD_LIBRARY_PATH;unset' 'LOADEDMODULES;unset' 'MPI_BIN;unset' 'MPI_COMPILER;unset' 'MPI_FORTRAN_MOD_DIR;unset' 'MPI_HOME;unset' 'MPI_INCLUDE;unset' 'MPI_LIB;unset' 'MPI_MAN;unset' 'MPI_PYTHON_SITEARCH;unset' 'MPI_SUFFIX;unset' 'MPI_SYSCONFIG;unset' 'PYTHONPATH;unset' '_LMFILES_;' ++ PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/bin ++ export PATH ++ unset LD_LIBRARY_PATH ++ unset LOADEDMODULES ++ unset MPI_BIN ++ unset MPI_COMPILER ++ unset MPI_FORTRAN_MOD_DIR ++ unset MPI_HOME ++ unset MPI_INCLUDE ++ unset MPI_LIB ++ unset MPI_MAN ++ unset MPI_PYTHON_SITEARCH ++ unset MPI_SUFFIX ++ unset MPI_SYSCONFIG ++ unset PYTHONPATH ++ unset _LMFILES_ + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.V9V9AB + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 ++ dirname /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 + cd gromacs-4.5.5 + LANG=C + export LANG + unset DISPLAY + rm -rf /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 + . /etc/profile.d/modules.sh ++++ /bin/ps -p 19644 -ocomm= +++ /bin/basename sh ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ MODULESHOME=/usr/share/Modules +++ export MODULESHOME +++ '[' '' = '' ']' +++ LOADEDMODULES= +++ export LOADEDMODULES +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module load openmpi-ppc64 ++ /usr/bin/modulecmd sh load openmpi-ppc64 + eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=openmpi-ppc64' ';export' 'LOADEDMODULES;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-ppc64' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-ppc64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-ppc64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-ppc64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/usr/lib64/python2.6/site-packages/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-ppc64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/bin' ';export' 'PATH;PYTHONPATH=/usr/lib64/python2.6/site-packages/openmpi' ';export' 'PYTHONPATH;_LMFILES_=/etc/modulefiles/openmpi-ppc64' ';export' '_LMFILES_;' ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ LOADEDMODULES=openmpi-ppc64 ++ export LOADEDMODULES ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ MPI_COMPILER=openmpi-ppc64 ++ export MPI_COMPILER ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-ppc64 ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_INCLUDE=/usr/include/openmpi-ppc64 ++ export MPI_INCLUDE ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ MPI_MAN=/usr/share/man/openmpi-ppc64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.6/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-ppc64 ++ export MPI_SYSCONFIG ++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/bin ++ export PATH ++ PYTHONPATH=/usr/lib64/python2.6/site-packages/openmpi ++ export PYTHONPATH ++ _LMFILES_=/etc/modulefiles/openmpi-ppc64 ++ export _LMFILES_ + export 'CFLAGS= -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + CFLAGS=' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mminimal-toc' + mkdir -p /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/bin /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/lib + cd openmpi-single + install -p -m 755 src/kernel/mdrun /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/bin/g_mdrun_openmpi + cp -a src/gmxlib/libgmx_openmpi.so src/gmxlib/libgmx_openmpi.so.6 src/kernel/libgmxpreprocess_openmpi.so src/kernel/libgmxpreprocess_openmpi.so.6 src/mdlib/libmd_openmpi.so src/mdlib/libmd_openmpi.so.6 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/lib/ + cd .. + cd openmpi-double + install -p -m 755 src/kernel/mdrun /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/bin/g_mdrun_openmpi_d + cp -a src/gmxlib/libgmx_openmpi_d.so src/gmxlib/libgmx_openmpi_d.so.6 src/kernel/libgmxpreprocess_openmpi_d.so src/kernel/libgmxpreprocess_openmpi_d.so.6 src/mdlib/libmd_openmpi_d.so src/mdlib/libmd_openmpi_d.so.6 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/lib/ + cd .. + . /etc/profile.d/modules.sh ++++ /bin/ps -p 19644 -ocomm= +++ /bin/basename sh ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ MODULESHOME=/usr/share/Modules +++ export MODULESHOME +++ '[' openmpi-ppc64 = '' ']' +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module unload openmpi-ppc64 ++ /usr/bin/modulecmd sh unload openmpi-ppc64 + eval PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/bin ';export' 'PATH;unset' 'LD_LIBRARY_PATH;unset' 'LOADEDMODULES;unset' 'MPI_BIN;unset' 'MPI_COMPILER;unset' 'MPI_FORTRAN_MOD_DIR;unset' 'MPI_HOME;unset' 'MPI_INCLUDE;unset' 'MPI_LIB;unset' 'MPI_MAN;unset' 'MPI_PYTHON_SITEARCH;unset' 'MPI_SUFFIX;unset' 'MPI_SYSCONFIG;unset' 'PYTHONPATH;unset' '_LMFILES_;' ++ PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/bin ++ export PATH ++ unset LD_LIBRARY_PATH ++ unset LOADEDMODULES ++ unset MPI_BIN ++ unset MPI_COMPILER ++ unset MPI_FORTRAN_MOD_DIR ++ unset MPI_HOME ++ unset MPI_INCLUDE ++ unset MPI_LIB ++ unset MPI_MAN ++ unset MPI_PYTHON_SITEARCH ++ unset MPI_SUFFIX ++ unset MPI_SYSCONFIG ++ unset PYTHONPATH ++ unset _LMFILES_ + cd single + make DESTDIR=/builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 'INSTALL=install -p' install /usr/bin/cmake -H/builddir/build/BUILD/gromacs-4.5.5 -B/builddir/build/BUILD/gromacs-4.5.5/single --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles/progress.make make -f CMakeFiles/Makefile2 all make[1]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/single/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/gmxlib/CMakeFiles/gmx.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 [ 58%] Built target gmx make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/single/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/mdlib/CMakeFiles/md.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 59 60 61 62 63 64 65 66 67 68 [ 68%] Built target md make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/gmxpreprocess.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 70 71 72 73 [ 72%] Built target gmxpreprocess make -f src/kernel/CMakeFiles/g_luck.dir/build.make src/kernel/CMakeFiles/g_luck.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_luck.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/g_luck.dir/build.make src/kernel/CMakeFiles/g_luck.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/g_luck.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 72%] Built target g_luck make -f src/kernel/CMakeFiles/g_protonate.dir/build.make src/kernel/CMakeFiles/g_protonate.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_protonate.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/g_protonate.dir/build.make src/kernel/CMakeFiles/g_protonate.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/g_protonate.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 72%] Built target g_protonate make -f src/kernel/CMakeFiles/g_x2top.dir/build.make src/kernel/CMakeFiles/g_x2top.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/g_x2top.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/g_x2top.dir/build.make src/kernel/CMakeFiles/g_x2top.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/g_x2top.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 72%] Built target g_x2top make -f src/kernel/CMakeFiles/gmxcheck.dir/build.make src/kernel/CMakeFiles/gmxcheck.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxcheck.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/gmxcheck.dir/build.make src/kernel/CMakeFiles/gmxcheck.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/gmxcheck.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 72%] Built target gmxcheck make -f src/kernel/CMakeFiles/gmxdump.dir/build.make src/kernel/CMakeFiles/gmxdump.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/gmxdump.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/gmxdump.dir/build.make src/kernel/CMakeFiles/gmxdump.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/gmxdump.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 69 [ 73%] Built target gmxdump make -f src/kernel/CMakeFiles/grompp.dir/build.make src/kernel/CMakeFiles/grompp.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/grompp.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/grompp.dir/build.make src/kernel/CMakeFiles/grompp.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/grompp.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 73%] Built target grompp make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/mdrun.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 74 [ 74%] Built target mdrun make -f src/kernel/CMakeFiles/pdb2gmx.dir/build.make src/kernel/CMakeFiles/pdb2gmx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/pdb2gmx.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/pdb2gmx.dir/build.make src/kernel/CMakeFiles/pdb2gmx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/pdb2gmx.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 75 [ 75%] Built target pdb2gmx make -f src/kernel/CMakeFiles/tpbconv.dir/build.make src/kernel/CMakeFiles/tpbconv.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel /builddir/build/BUILD/gromacs-4.5.5/single/src/kernel/CMakeFiles/tpbconv.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/kernel/CMakeFiles/tpbconv.dir/build.make src/kernel/CMakeFiles/tpbconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/kernel/CMakeFiles/tpbconv.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 75%] Built target tpbconv make -f src/tools/CMakeFiles/gmxana.dir/build.make src/tools/CMakeFiles/gmxana.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/gmxana.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/gmxana.dir/build.make src/tools/CMakeFiles/gmxana.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/gmxana.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 86 87 88 89 90 91 92 93 94 95 96 97 98 99 [ 89%] Built target gmxana make -f src/tools/CMakeFiles/do_dssp.dir/build.make src/tools/CMakeFiles/do_dssp.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/do_dssp.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/do_dssp.dir/build.make src/tools/CMakeFiles/do_dssp.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/do_dssp.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] Built target do_dssp make -f src/tools/CMakeFiles/editconf.dir/build.make src/tools/CMakeFiles/editconf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/editconf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/editconf.dir/build.make src/tools/CMakeFiles/editconf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/editconf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] Built target editconf make -f src/tools/CMakeFiles/eneconv.dir/build.make src/tools/CMakeFiles/eneconv.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/eneconv.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/eneconv.dir/build.make src/tools/CMakeFiles/eneconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/eneconv.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] Built target eneconv make -f src/tools/CMakeFiles/g_anadock.dir/build.make src/tools/CMakeFiles/g_anadock.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_anadock.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_anadock.dir/build.make src/tools/CMakeFiles/g_anadock.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_anadock.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] Built target g_anadock make -f src/tools/CMakeFiles/g_anaeig.dir/build.make src/tools/CMakeFiles/g_anaeig.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_anaeig.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_anaeig.dir/build.make src/tools/CMakeFiles/g_anaeig.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_anaeig.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] Built target g_anaeig make -f src/tools/CMakeFiles/g_analyze.dir/build.make src/tools/CMakeFiles/g_analyze.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_analyze.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_analyze.dir/build.make src/tools/CMakeFiles/g_analyze.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_analyze.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 89%] Built target g_analyze make -f src/tools/CMakeFiles/g_angle.dir/build.make src/tools/CMakeFiles/g_angle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_angle.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_angle.dir/build.make src/tools/CMakeFiles/g_angle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_angle.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 76 [ 90%] Built target g_angle make -f src/tools/CMakeFiles/g_bar.dir/build.make src/tools/CMakeFiles/g_bar.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bar.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_bar.dir/build.make src/tools/CMakeFiles/g_bar.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_bar.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Built target g_bar make -f src/tools/CMakeFiles/g_bond.dir/build.make src/tools/CMakeFiles/g_bond.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bond.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_bond.dir/build.make src/tools/CMakeFiles/g_bond.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_bond.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Built target g_bond make -f src/tools/CMakeFiles/g_bundle.dir/build.make src/tools/CMakeFiles/g_bundle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_bundle.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_bundle.dir/build.make src/tools/CMakeFiles/g_bundle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_bundle.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Built target g_bundle make -f src/tools/CMakeFiles/g_chi.dir/build.make src/tools/CMakeFiles/g_chi.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_chi.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_chi.dir/build.make src/tools/CMakeFiles/g_chi.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_chi.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Built target g_chi make -f src/tools/CMakeFiles/g_cluster.dir/build.make src/tools/CMakeFiles/g_cluster.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_cluster.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_cluster.dir/build.make src/tools/CMakeFiles/g_cluster.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_cluster.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Built target g_cluster make -f src/tools/CMakeFiles/g_clustsize.dir/build.make src/tools/CMakeFiles/g_clustsize.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_clustsize.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_clustsize.dir/build.make src/tools/CMakeFiles/g_clustsize.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_clustsize.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 90%] Built target g_clustsize make -f src/tools/CMakeFiles/g_confrms.dir/build.make src/tools/CMakeFiles/g_confrms.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_confrms.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_confrms.dir/build.make src/tools/CMakeFiles/g_confrms.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_confrms.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 77 [ 91%] Built target g_confrms make -f src/tools/CMakeFiles/g_covar.dir/build.make src/tools/CMakeFiles/g_covar.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_covar.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_covar.dir/build.make src/tools/CMakeFiles/g_covar.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_covar.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_covar make -f src/tools/CMakeFiles/g_current.dir/build.make src/tools/CMakeFiles/g_current.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_current.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_current.dir/build.make src/tools/CMakeFiles/g_current.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_current.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_current make -f src/tools/CMakeFiles/g_density.dir/build.make src/tools/CMakeFiles/g_density.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_density.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_density.dir/build.make src/tools/CMakeFiles/g_density.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_density.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_density make -f src/tools/CMakeFiles/g_densmap.dir/build.make src/tools/CMakeFiles/g_densmap.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_densmap.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_densmap.dir/build.make src/tools/CMakeFiles/g_densmap.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_densmap.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_densmap make -f src/tools/CMakeFiles/g_densorder.dir/build.make src/tools/CMakeFiles/g_densorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_densorder.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_densorder.dir/build.make src/tools/CMakeFiles/g_densorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_densorder.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_densorder make -f src/tools/CMakeFiles/g_dielectric.dir/build.make src/tools/CMakeFiles/g_dielectric.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dielectric.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dielectric.dir/build.make src/tools/CMakeFiles/g_dielectric.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dielectric.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_dielectric make -f src/tools/CMakeFiles/g_dih.dir/build.make src/tools/CMakeFiles/g_dih.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dih.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dih.dir/build.make src/tools/CMakeFiles/g_dih.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dih.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 91%] Built target g_dih make -f src/tools/CMakeFiles/g_dipoles.dir/build.make src/tools/CMakeFiles/g_dipoles.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dipoles.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dipoles.dir/build.make src/tools/CMakeFiles/g_dipoles.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dipoles.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 78 [ 92%] Built target g_dipoles make -f src/tools/CMakeFiles/g_disre.dir/build.make src/tools/CMakeFiles/g_disre.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_disre.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_disre.dir/build.make src/tools/CMakeFiles/g_disre.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_disre.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] Built target g_disre make -f src/tools/CMakeFiles/g_dist.dir/build.make src/tools/CMakeFiles/g_dist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dist.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dist.dir/build.make src/tools/CMakeFiles/g_dist.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dist.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] Built target g_dist make -f src/tools/CMakeFiles/g_dos.dir/build.make src/tools/CMakeFiles/g_dos.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dos.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dos.dir/build.make src/tools/CMakeFiles/g_dos.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dos.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] Built target g_dos make -f src/tools/CMakeFiles/g_dyndom.dir/build.make src/tools/CMakeFiles/g_dyndom.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_dyndom.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_dyndom.dir/build.make src/tools/CMakeFiles/g_dyndom.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dyndom.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] Built target g_dyndom make -f src/tools/CMakeFiles/g_enemat.dir/build.make src/tools/CMakeFiles/g_enemat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_enemat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_enemat.dir/build.make src/tools/CMakeFiles/g_enemat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_enemat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] Built target g_enemat make -f src/tools/CMakeFiles/g_energy.dir/build.make src/tools/CMakeFiles/g_energy.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_energy.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_energy.dir/build.make src/tools/CMakeFiles/g_energy.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_energy.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 92%] Built target g_energy make -f src/tools/CMakeFiles/g_filter.dir/build.make src/tools/CMakeFiles/g_filter.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_filter.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_filter.dir/build.make src/tools/CMakeFiles/g_filter.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_filter.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 79 [ 93%] Built target g_filter make -f src/tools/CMakeFiles/g_gyrate.dir/build.make src/tools/CMakeFiles/g_gyrate.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_gyrate.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_gyrate.dir/build.make src/tools/CMakeFiles/g_gyrate.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_gyrate.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_gyrate make -f src/tools/CMakeFiles/g_h2order.dir/build.make src/tools/CMakeFiles/g_h2order.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_h2order.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_h2order.dir/build.make src/tools/CMakeFiles/g_h2order.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_h2order.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_h2order make -f src/tools/CMakeFiles/g_hbond.dir/build.make src/tools/CMakeFiles/g_hbond.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_hbond.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_hbond.dir/build.make src/tools/CMakeFiles/g_hbond.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_hbond.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_hbond make -f src/tools/CMakeFiles/g_helix.dir/build.make src/tools/CMakeFiles/g_helix.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_helix.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_helix.dir/build.make src/tools/CMakeFiles/g_helix.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_helix.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_helix make -f src/tools/CMakeFiles/g_helixorient.dir/build.make src/tools/CMakeFiles/g_helixorient.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_helixorient.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_helixorient.dir/build.make src/tools/CMakeFiles/g_helixorient.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_helixorient.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_helixorient make -f src/tools/CMakeFiles/g_hydorder.dir/build.make src/tools/CMakeFiles/g_hydorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_hydorder.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_hydorder.dir/build.make src/tools/CMakeFiles/g_hydorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_hydorder.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_hydorder make -f src/tools/CMakeFiles/g_kinetics.dir/build.make src/tools/CMakeFiles/g_kinetics.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_kinetics.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_kinetics.dir/build.make src/tools/CMakeFiles/g_kinetics.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_kinetics.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 93%] Built target g_kinetics make -f src/tools/CMakeFiles/g_lie.dir/build.make src/tools/CMakeFiles/g_lie.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_lie.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_lie.dir/build.make src/tools/CMakeFiles/g_lie.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_lie.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 80 [ 94%] Built target g_lie make -f src/tools/CMakeFiles/g_mdmat.dir/build.make src/tools/CMakeFiles/g_mdmat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_mdmat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_mdmat.dir/build.make src/tools/CMakeFiles/g_mdmat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_mdmat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Built target g_mdmat make -f src/tools/CMakeFiles/g_membed.dir/build.make src/tools/CMakeFiles/g_membed.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_membed.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_membed.dir/build.make src/tools/CMakeFiles/g_membed.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_membed.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Built target g_membed make -f src/tools/CMakeFiles/g_mindist.dir/build.make src/tools/CMakeFiles/g_mindist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_mindist.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_mindist.dir/build.make src/tools/CMakeFiles/g_mindist.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_mindist.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Built target g_mindist make -f src/tools/CMakeFiles/g_morph.dir/build.make src/tools/CMakeFiles/g_morph.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_morph.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_morph.dir/build.make src/tools/CMakeFiles/g_morph.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_morph.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Built target g_morph make -f src/tools/CMakeFiles/g_msd.dir/build.make src/tools/CMakeFiles/g_msd.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_msd.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_msd.dir/build.make src/tools/CMakeFiles/g_msd.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_msd.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Built target g_msd make -f src/tools/CMakeFiles/g_nmeig.dir/build.make src/tools/CMakeFiles/g_nmeig.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_nmeig.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_nmeig.dir/build.make src/tools/CMakeFiles/g_nmeig.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_nmeig.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 94%] Built target g_nmeig make -f src/tools/CMakeFiles/g_nmens.dir/build.make src/tools/CMakeFiles/g_nmens.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_nmens.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_nmens.dir/build.make src/tools/CMakeFiles/g_nmens.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_nmens.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 81 [ 95%] Built target g_nmens make -f src/tools/CMakeFiles/g_nmtraj.dir/build.make src/tools/CMakeFiles/g_nmtraj.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_nmtraj.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_nmtraj.dir/build.make src/tools/CMakeFiles/g_nmtraj.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_nmtraj.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_nmtraj make -f src/tools/CMakeFiles/g_options.dir/build.make src/tools/CMakeFiles/g_options.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_options.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_options.dir/build.make src/tools/CMakeFiles/g_options.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_options.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_options make -f src/tools/CMakeFiles/g_order.dir/build.make src/tools/CMakeFiles/g_order.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_order.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_order.dir/build.make src/tools/CMakeFiles/g_order.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_order.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_order make -f src/tools/CMakeFiles/g_pme_error.dir/build.make src/tools/CMakeFiles/g_pme_error.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_pme_error.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_pme_error.dir/build.make src/tools/CMakeFiles/g_pme_error.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_pme_error.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_pme_error make -f src/tools/CMakeFiles/g_polystat.dir/build.make src/tools/CMakeFiles/g_polystat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_polystat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_polystat.dir/build.make src/tools/CMakeFiles/g_polystat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_polystat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_polystat make -f src/tools/CMakeFiles/g_potential.dir/build.make src/tools/CMakeFiles/g_potential.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_potential.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_potential.dir/build.make src/tools/CMakeFiles/g_potential.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_potential.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_potential make -f src/tools/CMakeFiles/g_principal.dir/build.make src/tools/CMakeFiles/g_principal.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_principal.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_principal.dir/build.make src/tools/CMakeFiles/g_principal.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_principal.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 95%] Built target g_principal make -f src/tools/CMakeFiles/g_rama.dir/build.make src/tools/CMakeFiles/g_rama.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rama.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rama.dir/build.make src/tools/CMakeFiles/g_rama.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rama.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 82 [ 96%] Built target g_rama make -f src/tools/CMakeFiles/g_rdf.dir/build.make src/tools/CMakeFiles/g_rdf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rdf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rdf.dir/build.make src/tools/CMakeFiles/g_rdf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rdf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Built target g_rdf make -f src/tools/CMakeFiles/g_rms.dir/build.make src/tools/CMakeFiles/g_rms.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rms.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rms.dir/build.make src/tools/CMakeFiles/g_rms.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rms.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Built target g_rms make -f src/tools/CMakeFiles/g_rmsdist.dir/build.make src/tools/CMakeFiles/g_rmsdist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rmsdist.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rmsdist.dir/build.make src/tools/CMakeFiles/g_rmsdist.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rmsdist.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Built target g_rmsdist make -f src/tools/CMakeFiles/g_rmsf.dir/build.make src/tools/CMakeFiles/g_rmsf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rmsf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rmsf.dir/build.make src/tools/CMakeFiles/g_rmsf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rmsf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Built target g_rmsf make -f src/tools/CMakeFiles/g_rotacf.dir/build.make src/tools/CMakeFiles/g_rotacf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rotacf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rotacf.dir/build.make src/tools/CMakeFiles/g_rotacf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rotacf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Built target g_rotacf make -f src/tools/CMakeFiles/g_rotmat.dir/build.make src/tools/CMakeFiles/g_rotmat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_rotmat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_rotmat.dir/build.make src/tools/CMakeFiles/g_rotmat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rotmat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 96%] Built target g_rotmat make -f src/tools/CMakeFiles/g_saltbr.dir/build.make src/tools/CMakeFiles/g_saltbr.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_saltbr.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_saltbr.dir/build.make src/tools/CMakeFiles/g_saltbr.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_saltbr.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 83 [ 97%] Built target g_saltbr make -f src/tools/CMakeFiles/g_sas.dir/build.make src/tools/CMakeFiles/g_sas.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sas.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sas.dir/build.make src/tools/CMakeFiles/g_sas.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sas.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] Built target g_sas make -f src/tools/CMakeFiles/g_select.dir/build.make src/tools/CMakeFiles/g_select.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_select.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_select.dir/build.make src/tools/CMakeFiles/g_select.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_select.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] Built target g_select make -f src/tools/CMakeFiles/g_sgangle.dir/build.make src/tools/CMakeFiles/g_sgangle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sgangle.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sgangle.dir/build.make src/tools/CMakeFiles/g_sgangle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sgangle.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] Built target g_sgangle make -f src/tools/CMakeFiles/g_sham.dir/build.make src/tools/CMakeFiles/g_sham.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sham.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sham.dir/build.make src/tools/CMakeFiles/g_sham.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sham.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] Built target g_sham make -f src/tools/CMakeFiles/g_sigeps.dir/build.make src/tools/CMakeFiles/g_sigeps.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sigeps.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sigeps.dir/build.make src/tools/CMakeFiles/g_sigeps.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sigeps.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] Built target g_sigeps make -f src/tools/CMakeFiles/g_sorient.dir/build.make src/tools/CMakeFiles/g_sorient.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_sorient.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_sorient.dir/build.make src/tools/CMakeFiles/g_sorient.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sorient.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 97%] Built target g_sorient make -f src/tools/CMakeFiles/g_spatial.dir/build.make src/tools/CMakeFiles/g_spatial.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_spatial.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_spatial.dir/build.make src/tools/CMakeFiles/g_spatial.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_spatial.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 84 [ 98%] Built target g_spatial make -f src/tools/CMakeFiles/g_spol.dir/build.make src/tools/CMakeFiles/g_spol.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_spol.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_spol.dir/build.make src/tools/CMakeFiles/g_spol.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_spol.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_spol make -f src/tools/CMakeFiles/g_tcaf.dir/build.make src/tools/CMakeFiles/g_tcaf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_tcaf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_tcaf.dir/build.make src/tools/CMakeFiles/g_tcaf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_tcaf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_tcaf make -f src/tools/CMakeFiles/g_traj.dir/build.make src/tools/CMakeFiles/g_traj.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_traj.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_traj.dir/build.make src/tools/CMakeFiles/g_traj.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_traj.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_traj make -f src/tools/CMakeFiles/g_tune_pme.dir/build.make src/tools/CMakeFiles/g_tune_pme.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_tune_pme.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_tune_pme.dir/build.make src/tools/CMakeFiles/g_tune_pme.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_tune_pme.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_tune_pme make -f src/tools/CMakeFiles/g_vanhove.dir/build.make src/tools/CMakeFiles/g_vanhove.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_vanhove.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_vanhove.dir/build.make src/tools/CMakeFiles/g_vanhove.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_vanhove.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_vanhove make -f src/tools/CMakeFiles/g_velacc.dir/build.make src/tools/CMakeFiles/g_velacc.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_velacc.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_velacc.dir/build.make src/tools/CMakeFiles/g_velacc.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_velacc.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_velacc make -f src/tools/CMakeFiles/g_wham.dir/build.make src/tools/CMakeFiles/g_wham.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_wham.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_wham.dir/build.make src/tools/CMakeFiles/g_wham.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_wham.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 98%] Built target g_wham make -f src/tools/CMakeFiles/g_wheel.dir/build.make src/tools/CMakeFiles/g_wheel.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/g_wheel.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/g_wheel.dir/build.make src/tools/CMakeFiles/g_wheel.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_wheel.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles 85 [ 99%] Built target g_wheel make -f src/tools/CMakeFiles/genbox.dir/build.make src/tools/CMakeFiles/genbox.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genbox.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/genbox.dir/build.make src/tools/CMakeFiles/genbox.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/genbox.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Built target genbox make -f src/tools/CMakeFiles/genconf.dir/build.make src/tools/CMakeFiles/genconf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genconf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/genconf.dir/build.make src/tools/CMakeFiles/genconf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/genconf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Built target genconf make -f src/tools/CMakeFiles/genion.dir/build.make src/tools/CMakeFiles/genion.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genion.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/genion.dir/build.make src/tools/CMakeFiles/genion.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/genion.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Built target genion make -f src/tools/CMakeFiles/genrestr.dir/build.make src/tools/CMakeFiles/genrestr.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/genrestr.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/genrestr.dir/build.make src/tools/CMakeFiles/genrestr.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/genrestr.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Built target genrestr make -f src/tools/CMakeFiles/make_edi.dir/build.make src/tools/CMakeFiles/make_edi.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/make_edi.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/make_edi.dir/build.make src/tools/CMakeFiles/make_edi.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/make_edi.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Built target make_edi make -f src/tools/CMakeFiles/make_ndx.dir/build.make src/tools/CMakeFiles/make_ndx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends 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directory `/builddir/build/BUILD/gromacs-4.5.5/single' cd /builddir/build/BUILD/gromacs-4.5.5/single && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/single /builddir/build/BUILD/gromacs-4.5.5/single/src/tools /builddir/build/BUILD/gromacs-4.5.5/single/src/tools/CMakeFiles/trjcat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' make -f src/tools/CMakeFiles/trjcat.dir/build.make src/tools/CMakeFiles/trjcat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/single' make[2]: Nothing to be done for `src/tools/CMakeFiles/trjcat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/single' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/single/CMakeFiles [ 99%] Built target trjcat make -f src/tools/CMakeFiles/trjconv.dir/build.make 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Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_tune_pme -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_vanhove -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_velacc -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_clustsize -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_mdmat -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_wham -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_sigeps -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_bar -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_membed -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_pme_error -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rmsdist -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rotmat -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_options -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_dos -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_hydorder -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_densorder -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/pkgconfig/libgmxana.pc -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.bash -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.zsh -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.csh -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.bash -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.zsh -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.csh -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/demux.pl -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/xplor2gmx.pl + cd .. + cd double + make DESTDIR=/builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 'INSTALL=install -p' install /usr/bin/cmake -H/builddir/build/BUILD/gromacs-4.5.5 -B/builddir/build/BUILD/gromacs-4.5.5/double --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles/progress.make make -f CMakeFiles/Makefile2 all make[1]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib /builddir/build/BUILD/gromacs-4.5.5/double/src/gmxlib/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/gmxlib/CMakeFiles/gmx.dir/build.make src/gmxlib/CMakeFiles/gmx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/gmxlib/CMakeFiles/gmx.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 [ 58%] Built target gmx make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib /builddir/build/BUILD/gromacs-4.5.5/double/src/mdlib/CMakeFiles/md.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/mdlib/CMakeFiles/md.dir/build.make src/mdlib/CMakeFiles/md.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/mdlib/CMakeFiles/md.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 59 60 61 62 63 64 65 66 67 68 [ 68%] Built target md make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxpreprocess.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/gmxpreprocess.dir/build.make src/kernel/CMakeFiles/gmxpreprocess.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/gmxpreprocess.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 70 71 72 73 [ 72%] Built target gmxpreprocess make -f src/kernel/CMakeFiles/g_luck.dir/build.make src/kernel/CMakeFiles/g_luck.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_luck.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/g_luck.dir/build.make src/kernel/CMakeFiles/g_luck.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/g_luck.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Built target g_luck make -f src/kernel/CMakeFiles/g_protonate.dir/build.make src/kernel/CMakeFiles/g_protonate.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_protonate.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/g_protonate.dir/build.make src/kernel/CMakeFiles/g_protonate.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/g_protonate.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Built target g_protonate make -f src/kernel/CMakeFiles/g_x2top.dir/build.make src/kernel/CMakeFiles/g_x2top.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/g_x2top.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/g_x2top.dir/build.make src/kernel/CMakeFiles/g_x2top.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/g_x2top.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Built target g_x2top make -f src/kernel/CMakeFiles/gmxcheck.dir/build.make src/kernel/CMakeFiles/gmxcheck.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxcheck.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/gmxcheck.dir/build.make src/kernel/CMakeFiles/gmxcheck.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/gmxcheck.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 72%] Built target gmxcheck make -f src/kernel/CMakeFiles/gmxdump.dir/build.make src/kernel/CMakeFiles/gmxdump.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/gmxdump.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/gmxdump.dir/build.make src/kernel/CMakeFiles/gmxdump.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/gmxdump.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 69 [ 73%] Built target gmxdump make -f src/kernel/CMakeFiles/grompp.dir/build.make src/kernel/CMakeFiles/grompp.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/grompp.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/grompp.dir/build.make src/kernel/CMakeFiles/grompp.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/grompp.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 73%] Built target grompp make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/mdrun.dir/build.make src/kernel/CMakeFiles/mdrun.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/mdrun.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 74 [ 74%] Built target mdrun make -f src/kernel/CMakeFiles/pdb2gmx.dir/build.make src/kernel/CMakeFiles/pdb2gmx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/pdb2gmx.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/pdb2gmx.dir/build.make src/kernel/CMakeFiles/pdb2gmx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/pdb2gmx.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 75 [ 75%] Built target pdb2gmx make -f src/kernel/CMakeFiles/tpbconv.dir/build.make src/kernel/CMakeFiles/tpbconv.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel /builddir/build/BUILD/gromacs-4.5.5/double/src/kernel/CMakeFiles/tpbconv.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/kernel/CMakeFiles/tpbconv.dir/build.make src/kernel/CMakeFiles/tpbconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/kernel/CMakeFiles/tpbconv.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 75%] Built target tpbconv make -f src/tools/CMakeFiles/gmxana.dir/build.make src/tools/CMakeFiles/gmxana.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/gmxana.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/gmxana.dir/build.make src/tools/CMakeFiles/gmxana.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/gmxana.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 86 87 88 89 90 91 92 93 94 95 96 97 98 99 [ 89%] Built target gmxana make -f src/tools/CMakeFiles/do_dssp.dir/build.make src/tools/CMakeFiles/do_dssp.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/do_dssp.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/do_dssp.dir/build.make src/tools/CMakeFiles/do_dssp.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/do_dssp.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 89%] Built target do_dssp make -f src/tools/CMakeFiles/editconf.dir/build.make src/tools/CMakeFiles/editconf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/editconf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/editconf.dir/build.make src/tools/CMakeFiles/editconf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/editconf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 89%] Built target editconf make -f src/tools/CMakeFiles/eneconv.dir/build.make src/tools/CMakeFiles/eneconv.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/eneconv.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/eneconv.dir/build.make src/tools/CMakeFiles/eneconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/eneconv.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 89%] Built target eneconv make -f src/tools/CMakeFiles/g_anadock.dir/build.make src/tools/CMakeFiles/g_anadock.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_anadock.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_anadock.dir/build.make src/tools/CMakeFiles/g_anadock.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_anadock.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 89%] Built target g_anadock make -f src/tools/CMakeFiles/g_anaeig.dir/build.make src/tools/CMakeFiles/g_anaeig.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_anaeig.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_anaeig.dir/build.make src/tools/CMakeFiles/g_anaeig.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_anaeig.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 89%] Built target g_anaeig make -f src/tools/CMakeFiles/g_analyze.dir/build.make src/tools/CMakeFiles/g_analyze.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_analyze.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_analyze.dir/build.make src/tools/CMakeFiles/g_analyze.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_analyze.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 89%] Built target g_analyze make -f src/tools/CMakeFiles/g_angle.dir/build.make src/tools/CMakeFiles/g_angle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_angle.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_angle.dir/build.make src/tools/CMakeFiles/g_angle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_angle.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 76 [ 90%] Built target g_angle make -f src/tools/CMakeFiles/g_bar.dir/build.make src/tools/CMakeFiles/g_bar.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bar.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_bar.dir/build.make src/tools/CMakeFiles/g_bar.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_bar.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Built target g_bar make -f src/tools/CMakeFiles/g_bond.dir/build.make src/tools/CMakeFiles/g_bond.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bond.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_bond.dir/build.make src/tools/CMakeFiles/g_bond.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_bond.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Built target g_bond make -f src/tools/CMakeFiles/g_bundle.dir/build.make src/tools/CMakeFiles/g_bundle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_bundle.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_bundle.dir/build.make src/tools/CMakeFiles/g_bundle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_bundle.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Built target g_bundle make -f src/tools/CMakeFiles/g_chi.dir/build.make src/tools/CMakeFiles/g_chi.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_chi.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_chi.dir/build.make src/tools/CMakeFiles/g_chi.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_chi.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Built target g_chi make -f src/tools/CMakeFiles/g_cluster.dir/build.make src/tools/CMakeFiles/g_cluster.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_cluster.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_cluster.dir/build.make src/tools/CMakeFiles/g_cluster.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_cluster.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Built target g_cluster make -f src/tools/CMakeFiles/g_clustsize.dir/build.make src/tools/CMakeFiles/g_clustsize.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_clustsize.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_clustsize.dir/build.make src/tools/CMakeFiles/g_clustsize.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_clustsize.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 90%] Built target g_clustsize make -f src/tools/CMakeFiles/g_confrms.dir/build.make src/tools/CMakeFiles/g_confrms.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_confrms.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_confrms.dir/build.make src/tools/CMakeFiles/g_confrms.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_confrms.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 77 [ 91%] Built target g_confrms make -f src/tools/CMakeFiles/g_covar.dir/build.make src/tools/CMakeFiles/g_covar.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_covar.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_covar.dir/build.make src/tools/CMakeFiles/g_covar.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_covar.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_covar make -f src/tools/CMakeFiles/g_current.dir/build.make src/tools/CMakeFiles/g_current.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_current.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_current.dir/build.make src/tools/CMakeFiles/g_current.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_current.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_current make -f src/tools/CMakeFiles/g_density.dir/build.make src/tools/CMakeFiles/g_density.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_density.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_density.dir/build.make src/tools/CMakeFiles/g_density.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_density.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_density make -f src/tools/CMakeFiles/g_densmap.dir/build.make src/tools/CMakeFiles/g_densmap.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_densmap.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_densmap.dir/build.make src/tools/CMakeFiles/g_densmap.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_densmap.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_densmap make -f src/tools/CMakeFiles/g_densorder.dir/build.make src/tools/CMakeFiles/g_densorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_densorder.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_densorder.dir/build.make src/tools/CMakeFiles/g_densorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_densorder.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_densorder make -f src/tools/CMakeFiles/g_dielectric.dir/build.make src/tools/CMakeFiles/g_dielectric.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dielectric.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dielectric.dir/build.make src/tools/CMakeFiles/g_dielectric.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dielectric.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_dielectric make -f src/tools/CMakeFiles/g_dih.dir/build.make src/tools/CMakeFiles/g_dih.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dih.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dih.dir/build.make src/tools/CMakeFiles/g_dih.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dih.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 91%] Built target g_dih make -f src/tools/CMakeFiles/g_dipoles.dir/build.make src/tools/CMakeFiles/g_dipoles.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dipoles.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dipoles.dir/build.make src/tools/CMakeFiles/g_dipoles.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dipoles.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 78 [ 92%] Built target g_dipoles make -f src/tools/CMakeFiles/g_disre.dir/build.make src/tools/CMakeFiles/g_disre.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_disre.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_disre.dir/build.make src/tools/CMakeFiles/g_disre.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_disre.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Built target g_disre make -f src/tools/CMakeFiles/g_dist.dir/build.make src/tools/CMakeFiles/g_dist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dist.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dist.dir/build.make src/tools/CMakeFiles/g_dist.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dist.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Built target g_dist make -f src/tools/CMakeFiles/g_dos.dir/build.make src/tools/CMakeFiles/g_dos.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dos.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dos.dir/build.make src/tools/CMakeFiles/g_dos.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dos.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Built target g_dos make -f src/tools/CMakeFiles/g_dyndom.dir/build.make src/tools/CMakeFiles/g_dyndom.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_dyndom.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_dyndom.dir/build.make src/tools/CMakeFiles/g_dyndom.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_dyndom.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Built target g_dyndom make -f src/tools/CMakeFiles/g_enemat.dir/build.make src/tools/CMakeFiles/g_enemat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_enemat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_enemat.dir/build.make src/tools/CMakeFiles/g_enemat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_enemat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Built target g_enemat make -f src/tools/CMakeFiles/g_energy.dir/build.make src/tools/CMakeFiles/g_energy.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_energy.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_energy.dir/build.make src/tools/CMakeFiles/g_energy.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_energy.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 92%] Built target g_energy make -f src/tools/CMakeFiles/g_filter.dir/build.make src/tools/CMakeFiles/g_filter.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_filter.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_filter.dir/build.make src/tools/CMakeFiles/g_filter.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_filter.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 79 [ 93%] Built target g_filter make -f src/tools/CMakeFiles/g_gyrate.dir/build.make src/tools/CMakeFiles/g_gyrate.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_gyrate.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_gyrate.dir/build.make src/tools/CMakeFiles/g_gyrate.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_gyrate.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Built target g_gyrate make -f src/tools/CMakeFiles/g_h2order.dir/build.make src/tools/CMakeFiles/g_h2order.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_h2order.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_h2order.dir/build.make src/tools/CMakeFiles/g_h2order.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_h2order.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Built target g_h2order make -f src/tools/CMakeFiles/g_hbond.dir/build.make src/tools/CMakeFiles/g_hbond.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_hbond.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_hbond.dir/build.make src/tools/CMakeFiles/g_hbond.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_hbond.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Built target g_hbond make -f src/tools/CMakeFiles/g_helix.dir/build.make src/tools/CMakeFiles/g_helix.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_helix.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_helix.dir/build.make src/tools/CMakeFiles/g_helix.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_helix.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Built target g_helix make -f src/tools/CMakeFiles/g_helixorient.dir/build.make src/tools/CMakeFiles/g_helixorient.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_helixorient.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_helixorient.dir/build.make src/tools/CMakeFiles/g_helixorient.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_helixorient.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Built target g_helixorient make -f src/tools/CMakeFiles/g_hydorder.dir/build.make src/tools/CMakeFiles/g_hydorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_hydorder.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_hydorder.dir/build.make src/tools/CMakeFiles/g_hydorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_hydorder.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Built target g_hydorder make -f src/tools/CMakeFiles/g_kinetics.dir/build.make src/tools/CMakeFiles/g_kinetics.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_kinetics.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_kinetics.dir/build.make src/tools/CMakeFiles/g_kinetics.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_kinetics.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 93%] Built target g_kinetics make -f src/tools/CMakeFiles/g_lie.dir/build.make src/tools/CMakeFiles/g_lie.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_lie.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_lie.dir/build.make src/tools/CMakeFiles/g_lie.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_lie.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 80 [ 94%] Built target g_lie make -f src/tools/CMakeFiles/g_mdmat.dir/build.make src/tools/CMakeFiles/g_mdmat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_mdmat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_mdmat.dir/build.make src/tools/CMakeFiles/g_mdmat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_mdmat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] Built target g_mdmat make -f src/tools/CMakeFiles/g_membed.dir/build.make src/tools/CMakeFiles/g_membed.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_membed.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_membed.dir/build.make src/tools/CMakeFiles/g_membed.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_membed.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] Built target g_membed make -f src/tools/CMakeFiles/g_mindist.dir/build.make src/tools/CMakeFiles/g_mindist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_mindist.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_mindist.dir/build.make src/tools/CMakeFiles/g_mindist.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_mindist.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] Built target g_mindist make -f src/tools/CMakeFiles/g_morph.dir/build.make src/tools/CMakeFiles/g_morph.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_morph.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_morph.dir/build.make src/tools/CMakeFiles/g_morph.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_morph.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] Built target g_morph make -f src/tools/CMakeFiles/g_msd.dir/build.make src/tools/CMakeFiles/g_msd.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_msd.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_msd.dir/build.make src/tools/CMakeFiles/g_msd.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_msd.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] Built target g_msd make -f src/tools/CMakeFiles/g_nmeig.dir/build.make src/tools/CMakeFiles/g_nmeig.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmeig.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_nmeig.dir/build.make src/tools/CMakeFiles/g_nmeig.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_nmeig.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 94%] Built target g_nmeig make -f src/tools/CMakeFiles/g_nmens.dir/build.make src/tools/CMakeFiles/g_nmens.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmens.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_nmens.dir/build.make src/tools/CMakeFiles/g_nmens.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_nmens.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 81 [ 95%] Built target g_nmens make -f src/tools/CMakeFiles/g_nmtraj.dir/build.make src/tools/CMakeFiles/g_nmtraj.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_nmtraj.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_nmtraj.dir/build.make src/tools/CMakeFiles/g_nmtraj.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_nmtraj.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_nmtraj make -f src/tools/CMakeFiles/g_options.dir/build.make src/tools/CMakeFiles/g_options.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_options.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_options.dir/build.make src/tools/CMakeFiles/g_options.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_options.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_options make -f src/tools/CMakeFiles/g_order.dir/build.make src/tools/CMakeFiles/g_order.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_order.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_order.dir/build.make src/tools/CMakeFiles/g_order.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_order.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_order make -f src/tools/CMakeFiles/g_pme_error.dir/build.make src/tools/CMakeFiles/g_pme_error.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_pme_error.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_pme_error.dir/build.make src/tools/CMakeFiles/g_pme_error.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_pme_error.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_pme_error make -f src/tools/CMakeFiles/g_polystat.dir/build.make src/tools/CMakeFiles/g_polystat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_polystat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_polystat.dir/build.make src/tools/CMakeFiles/g_polystat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_polystat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_polystat make -f src/tools/CMakeFiles/g_potential.dir/build.make src/tools/CMakeFiles/g_potential.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_potential.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_potential.dir/build.make src/tools/CMakeFiles/g_potential.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_potential.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_potential make -f src/tools/CMakeFiles/g_principal.dir/build.make src/tools/CMakeFiles/g_principal.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_principal.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_principal.dir/build.make src/tools/CMakeFiles/g_principal.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_principal.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 95%] Built target g_principal make -f src/tools/CMakeFiles/g_rama.dir/build.make src/tools/CMakeFiles/g_rama.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rama.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rama.dir/build.make src/tools/CMakeFiles/g_rama.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rama.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 82 [ 96%] Built target g_rama make -f src/tools/CMakeFiles/g_rdf.dir/build.make src/tools/CMakeFiles/g_rdf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rdf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rdf.dir/build.make src/tools/CMakeFiles/g_rdf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rdf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_rdf make -f src/tools/CMakeFiles/g_rms.dir/build.make src/tools/CMakeFiles/g_rms.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rms.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rms.dir/build.make src/tools/CMakeFiles/g_rms.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rms.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_rms make -f src/tools/CMakeFiles/g_rmsdist.dir/build.make src/tools/CMakeFiles/g_rmsdist.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rmsdist.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rmsdist.dir/build.make src/tools/CMakeFiles/g_rmsdist.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rmsdist.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_rmsdist make -f src/tools/CMakeFiles/g_rmsf.dir/build.make src/tools/CMakeFiles/g_rmsf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rmsf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rmsf.dir/build.make src/tools/CMakeFiles/g_rmsf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rmsf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_rmsf make -f src/tools/CMakeFiles/g_rotacf.dir/build.make src/tools/CMakeFiles/g_rotacf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rotacf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rotacf.dir/build.make src/tools/CMakeFiles/g_rotacf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rotacf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_rotacf make -f src/tools/CMakeFiles/g_rotmat.dir/build.make src/tools/CMakeFiles/g_rotmat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_rotmat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_rotmat.dir/build.make src/tools/CMakeFiles/g_rotmat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_rotmat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 96%] Built target g_rotmat make -f src/tools/CMakeFiles/g_saltbr.dir/build.make src/tools/CMakeFiles/g_saltbr.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_saltbr.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_saltbr.dir/build.make src/tools/CMakeFiles/g_saltbr.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_saltbr.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 83 [ 97%] Built target g_saltbr make -f src/tools/CMakeFiles/g_sas.dir/build.make src/tools/CMakeFiles/g_sas.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sas.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sas.dir/build.make src/tools/CMakeFiles/g_sas.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sas.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] Built target g_sas make -f src/tools/CMakeFiles/g_select.dir/build.make src/tools/CMakeFiles/g_select.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_select.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_select.dir/build.make src/tools/CMakeFiles/g_select.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_select.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] Built target g_select make -f src/tools/CMakeFiles/g_sgangle.dir/build.make src/tools/CMakeFiles/g_sgangle.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sgangle.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sgangle.dir/build.make src/tools/CMakeFiles/g_sgangle.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sgangle.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] Built target g_sgangle make -f src/tools/CMakeFiles/g_sham.dir/build.make src/tools/CMakeFiles/g_sham.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sham.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sham.dir/build.make src/tools/CMakeFiles/g_sham.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sham.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] Built target g_sham make -f src/tools/CMakeFiles/g_sigeps.dir/build.make src/tools/CMakeFiles/g_sigeps.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sigeps.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sigeps.dir/build.make src/tools/CMakeFiles/g_sigeps.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sigeps.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] Built target g_sigeps make -f src/tools/CMakeFiles/g_sorient.dir/build.make src/tools/CMakeFiles/g_sorient.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_sorient.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_sorient.dir/build.make src/tools/CMakeFiles/g_sorient.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_sorient.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 97%] Built target g_sorient make -f src/tools/CMakeFiles/g_spatial.dir/build.make src/tools/CMakeFiles/g_spatial.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_spatial.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_spatial.dir/build.make src/tools/CMakeFiles/g_spatial.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_spatial.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 84 [ 98%] Built target g_spatial make -f src/tools/CMakeFiles/g_spol.dir/build.make src/tools/CMakeFiles/g_spol.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_spol.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_spol.dir/build.make src/tools/CMakeFiles/g_spol.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_spol.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_spol make -f src/tools/CMakeFiles/g_tcaf.dir/build.make src/tools/CMakeFiles/g_tcaf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_tcaf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_tcaf.dir/build.make src/tools/CMakeFiles/g_tcaf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_tcaf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_tcaf make -f src/tools/CMakeFiles/g_traj.dir/build.make src/tools/CMakeFiles/g_traj.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_traj.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_traj.dir/build.make src/tools/CMakeFiles/g_traj.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_traj.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_traj make -f src/tools/CMakeFiles/g_tune_pme.dir/build.make src/tools/CMakeFiles/g_tune_pme.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_tune_pme.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_tune_pme.dir/build.make src/tools/CMakeFiles/g_tune_pme.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_tune_pme.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_tune_pme make -f src/tools/CMakeFiles/g_vanhove.dir/build.make src/tools/CMakeFiles/g_vanhove.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_vanhove.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_vanhove.dir/build.make src/tools/CMakeFiles/g_vanhove.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_vanhove.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_vanhove make -f src/tools/CMakeFiles/g_velacc.dir/build.make src/tools/CMakeFiles/g_velacc.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_velacc.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_velacc.dir/build.make src/tools/CMakeFiles/g_velacc.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_velacc.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_velacc make -f src/tools/CMakeFiles/g_wham.dir/build.make src/tools/CMakeFiles/g_wham.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_wham.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_wham.dir/build.make src/tools/CMakeFiles/g_wham.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_wham.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 98%] Built target g_wham make -f src/tools/CMakeFiles/g_wheel.dir/build.make src/tools/CMakeFiles/g_wheel.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/g_wheel.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/g_wheel.dir/build.make src/tools/CMakeFiles/g_wheel.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/g_wheel.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 85 [ 99%] Built target g_wheel make -f src/tools/CMakeFiles/genbox.dir/build.make src/tools/CMakeFiles/genbox.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genbox.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/genbox.dir/build.make src/tools/CMakeFiles/genbox.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/genbox.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target genbox make -f src/tools/CMakeFiles/genconf.dir/build.make src/tools/CMakeFiles/genconf.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genconf.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/genconf.dir/build.make src/tools/CMakeFiles/genconf.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/genconf.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target genconf make -f src/tools/CMakeFiles/genion.dir/build.make src/tools/CMakeFiles/genion.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genion.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/genion.dir/build.make src/tools/CMakeFiles/genion.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/genion.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target genion make -f src/tools/CMakeFiles/genrestr.dir/build.make src/tools/CMakeFiles/genrestr.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/genrestr.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/genrestr.dir/build.make src/tools/CMakeFiles/genrestr.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/genrestr.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target genrestr make -f src/tools/CMakeFiles/make_edi.dir/build.make src/tools/CMakeFiles/make_edi.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/make_edi.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/make_edi.dir/build.make src/tools/CMakeFiles/make_edi.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/make_edi.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target make_edi make -f src/tools/CMakeFiles/make_ndx.dir/build.make src/tools/CMakeFiles/make_ndx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/make_ndx.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/make_ndx.dir/build.make src/tools/CMakeFiles/make_ndx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/make_ndx.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target make_ndx make -f src/tools/CMakeFiles/mk_angndx.dir/build.make src/tools/CMakeFiles/mk_angndx.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/mk_angndx.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/mk_angndx.dir/build.make src/tools/CMakeFiles/mk_angndx.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/mk_angndx.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target mk_angndx make -f src/tools/CMakeFiles/trjcat.dir/build.make src/tools/CMakeFiles/trjcat.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjcat.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/trjcat.dir/build.make src/tools/CMakeFiles/trjcat.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/trjcat.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target trjcat make -f src/tools/CMakeFiles/trjconv.dir/build.make src/tools/CMakeFiles/trjconv.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjconv.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/trjconv.dir/build.make src/tools/CMakeFiles/trjconv.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/trjconv.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target trjconv make -f src/tools/CMakeFiles/trjorder.dir/build.make src/tools/CMakeFiles/trjorder.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/trjorder.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/trjorder.dir/build.make src/tools/CMakeFiles/trjorder.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/trjorder.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles [ 99%] Built target trjorder make -f src/tools/CMakeFiles/xpm2ps.dir/build.make src/tools/CMakeFiles/xpm2ps.dir/depend make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' cd /builddir/build/BUILD/gromacs-4.5.5/double && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/gromacs-4.5.5 /builddir/build/BUILD/gromacs-4.5.5/src/tools /builddir/build/BUILD/gromacs-4.5.5/double /builddir/build/BUILD/gromacs-4.5.5/double/src/tools /builddir/build/BUILD/gromacs-4.5.5/double/src/tools/CMakeFiles/xpm2ps.dir/DependInfo.cmake --color= make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' make -f src/tools/CMakeFiles/xpm2ps.dir/build.make src/tools/CMakeFiles/xpm2ps.dir/build make[2]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[2]: Nothing to be done for `src/tools/CMakeFiles/xpm2ps.dir/build'. make[2]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_report /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 100 [100%] Built target xpm2ps make[1]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/gromacs-4.5.5/double/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory `/builddir/build/BUILD/gromacs-4.5.5/double' make[1]: Nothing to be done for `preinstall'. make[1]: Leaving directory `/builddir/build/BUILD/gromacs-4.5.5/double' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/gromacs/. -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/gromacs/./html -- 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/builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/genbox.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_dielectric.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_vanhove.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_sham.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/trjcat.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_density.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_order.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/trjorder.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_nmens.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/mk_angndx.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_bundle.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_current.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_h2order.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_velacc.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_angle.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_wham.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_analyze.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_nmeig.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_tcaf.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_spatial.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_sigeps.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_hbond.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_dih.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/eneconv.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_x2top.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/pdb2gmx.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_rotacf.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_disre.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_rmsf.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/ngmx.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_dipoles.1 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man1/g_spol.1 -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man7 -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/./man7/gromacs.7 -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libgmx_d.so.6 -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libgmx_d.so -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/pkgconfig/libgmx_d.pc -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libmd_d.so.6 -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libmd_d.so -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/pkgconfig/libmd_d.pc -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libgmxpreprocess_d.so.6 -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libgmxpreprocess_d.so -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/mdrun_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/grompp_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/tpbconv_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/pdb2gmx_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_protonate_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_luck_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/gmxdump_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_x2top_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/gmxcheck_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/pkgconfig/libgmxpreprocess_d.pc -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libgmxana_d.so.6 -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libgmxana_d.so -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/do_dssp_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/editconf_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/eneconv_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genbox_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genconf_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genrestr_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_nmtraj_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/make_ndx_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/mk_angndx_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjcat_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjconv_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjorder_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_wheel_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/xpm2ps_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genion_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_anadock_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/make_edi_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_analyze_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_anaeig_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_angle_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_bond_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_bundle_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_chi_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_cluster_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_confrms_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_covar_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_current_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_density_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_densmap_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_dih_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_dielectric_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_helixorient_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_principal_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_dipoles_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_disre_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_dist_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_dyndom_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_enemat_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_energy_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_lie_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_filter_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_gyrate_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_h2order_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_hbond_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_helix_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_mindist_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_msd_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_morph_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_nmeig_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_nmens_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_order_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_kinetics_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_polystat_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_potential_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rama_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rdf_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rms_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rmsf_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rotacf_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_saltbr_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_sas_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_select_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_sgangle_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_sham_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_sorient_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_spol_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_spatial_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_tcaf_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_traj_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_tune_pme_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_vanhove_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_velacc_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_clustsize_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_mdmat_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_wham_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_sigeps_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_bar_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_membed_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_pme_error_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rmsdist_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rotmat_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_options_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_dos_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_hydorder_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_densorder_d -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/pkgconfig/libgmxana_d.pc -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.bash -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.zsh -- Installing: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.csh -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.bash -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.zsh -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.csh -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/demux.pl -- Up-to-date: /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/xplor2gmx.pl + cd .. + install -cpm 644 /builddir/build/SOURCES/manual-4.5.4.pdf . + install -cpm 644 /builddir/build/SOURCES/gromacs-README.fedora README.fedora + rm -rf '/builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/gromacs/template/Makefil*' + install -cpm 644 /builddir/build/SOURCES/gromacs-template-makefile-single /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/gromacs/template/Makefile.single + install -cpm 644 /builddir/build/SOURCES/gromacs-template-makefile-double /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/gromacs/template/Makefile.double + install -cpm 644 /builddir/build/SOURCES/gromacs-template-makefile-mpi-single /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/gromacs/template/Makefile.mpi.single + install -cpm 644 /builddir/build/SOURCES/gromacs-template-makefile-mpi-double /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/gromacs/template/Makefile.mpi.double + chmod a+x /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.bash /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.csh /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/GMXRC.zsh + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/do_dssp /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_do_dssp + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/do_dssp_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_do_dssp_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/editconf /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_editconf + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/editconf_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_editconf_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/eneconv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_eneconv + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/eneconv_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_eneconv_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genbox /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_genbox + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genbox_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_genbox_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genconf /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_genconf + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genconf_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_genconf_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genion /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_genion + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genion_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_genion_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genrestr /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_genrestr + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/genrestr_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_genrestr_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/gmxcheck /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_gmxcheck + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/gmxcheck_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_gmxcheck_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/gmxdump /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_gmxdump + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/gmxdump_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_gmxdump_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/grompp /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_grompp + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/grompp_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_grompp_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/make_edi /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_make_edi + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/make_edi_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_make_edi_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/make_ndx /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_make_ndx + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/make_ndx_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_make_ndx_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/mdrun /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_mdrun + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/mdrun_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_mdrun_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/mk_angndx /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_mk_angndx + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/mk_angndx_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_mk_angndx_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/pdb2gmx /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_pdb2gmx + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/pdb2gmx_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_pdb2gmx_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/tpbconv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_tpbconv + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/tpbconv_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_tpbconv_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjcat /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_trjcat + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjcat_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_trjcat_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjconv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_trjconv + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjconv_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_trjconv_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjorder /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_trjorder + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/trjorder_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_trjorder_d + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/xpm2ps /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/xpm2ps_d /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_xpm2ps_d + for bin in demux.pl xplor2gmx.pl + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/demux.pl /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_demux.pl + for bin in demux.pl xplor2gmx.pl + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/xplor2gmx.pl /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_xplor2gmx.pl + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/do_dssp.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_do_dssp.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/editconf.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_editconf.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/eneconv.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_eneconv.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/genbox.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_genbox.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/genconf.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_genconf.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/genion.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_genion.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/genrestr.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_genrestr.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/gmxcheck.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_gmxcheck.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/gmxdump.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_gmxdump.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/grompp.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_grompp.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/make_edi.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_make_edi.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/make_ndx.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_make_ndx.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/mdrun.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_mdrun.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/mk_angndx.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_mk_angndx.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/pdb2gmx.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_pdb2gmx.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/tpbconv.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_tpbconv.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/trjcat.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_trjcat.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/trjconv.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_trjconv.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/trjorder.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_trjorder.1 + for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/xpm2ps.1 /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/man/man1/g_xpm2ps.1 + chmod a-x /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.bash /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.csh /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.zsh + mkdir -p /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/zsh/site-functions + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.zsh /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/zsh/site-functions/gromacs + mkdir -p /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/etc/bash_completion.d + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.bash /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/etc/bash_completion.d/gromacs + mv /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/completion.csh . + find /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 -name '*.la' -exec rm -rf '{}' ';' + find /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 -name '*.so.*' -exec execstack -c '{}' ';' + /usr/lib/rpm/find-debuginfo.sh --strict-build-id /builddir/build/BUILD/gromacs-4.5.5 extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_mdmat extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_energy extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_anaeig extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_rmsdist_d extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_hydorder_d extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_density_d extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_analyze extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_helix extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/bin/g_sorient extracting debug info from 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debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/lib/libgmxpreprocess_openmpi.so.6 extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/lib/libmd_openmpi_d.so.6 extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/lib/libgmx_openmpi.so.6 extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/openmpi/lib/libgmxpreprocess_openmpi_d.so.6 extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libmd.so.6 extracting debug info from /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/lib64/libgmx_d.so.6 symlinked /usr/lib/debug/usr/lib64/openmpi/lib/libmd_openmpi.so.6.debug to /usr/lib/debug/usr/lib64/openmpi/lib/libmd_openmpi.so.debug symlinked /usr/lib/debug/usr/lib64/openmpi/lib/libgmx_openmpi_d.so.6.debug to /usr/lib/debug/usr/lib64/openmpi/lib/libgmx_openmpi_d.so.debug symlinked /usr/lib/debug/usr/lib64/openmpi/lib/libgmxpreprocess_openmpi.so.6.debug to /usr/lib/debug/usr/lib64/openmpi/lib/libgmxpreprocess_openmpi.so.debug symlinked /usr/lib/debug/usr/lib64/openmpi/lib/libgmxpreprocess_openmpi_d.so.6.debug to /usr/lib/debug/usr/lib64/openmpi/lib/libgmxpreprocess_openmpi_d.so.debug symlinked /usr/lib/debug/usr/lib64/openmpi/lib/libgmx_openmpi.so.6.debug to /usr/lib/debug/usr/lib64/openmpi/lib/libgmx_openmpi.so.debug symlinked /usr/lib/debug/usr/lib64/openmpi/lib/libmd_openmpi_d.so.6.debug to /usr/lib/debug/usr/lib64/openmpi/lib/libmd_openmpi_d.so.debug symlinked /usr/lib/debug/usr/lib64/libgmxana_d.so.6.debug to /usr/lib/debug/usr/lib64/libgmxana_d.so.debug symlinked /usr/lib/debug/usr/lib64/libgmx.so.6.debug to /usr/lib/debug/usr/lib64/libgmx.so.debug symlinked /usr/lib/debug/usr/lib64/libgmxpreprocess.so.6.debug to /usr/lib/debug/usr/lib64/libgmxpreprocess.so.debug symlinked /usr/lib/debug/usr/lib64/libgmxpreprocess_d.so.6.debug to /usr/lib/debug/usr/lib64/libgmxpreprocess_d.so.debug symlinked /usr/lib/debug/usr/lib64/libgmxana.so.6.debug to /usr/lib/debug/usr/lib64/libgmxana.so.debug symlinked /usr/lib/debug/usr/lib64/libmd_d.so.6.debug to /usr/lib/debug/usr/lib64/libmd_d.so.debug symlinked /usr/lib/debug/usr/lib64/libgmx_d.so.6.debug to /usr/lib/debug/usr/lib64/libgmx_d.so.debug symlinked /usr/lib/debug/usr/lib64/libmd.so.6.debug to /usr/lib/debug/usr/lib64/libmd.so.debug cpio: gromacs-4.5.5/double/src/gmxlib/parser.c: Cannot stat: No such file or directory cpio: gromacs-4.5.5/double/src/gmxlib/parser.h: Cannot stat: No such file or directory cpio: gromacs-4.5.5/double/src/gmxlib/parser.y: Cannot stat: No such file or directory cpio: gromacs-4.5.5/double/src/gmxlib/scanner.c: Cannot stat: No such file or directory cpio: gromacs-4.5.5/double/src/gmxlib/scanner.l: Cannot stat: No such file or directory cpio: gromacs-4.5.5/double/src/gmxlib/scanner_flex.h: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-double/src/gmxlib/parser.c: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-double/src/gmxlib/parser.h: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-double/src/gmxlib/parser.y: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-double/src/gmxlib/scanner.c: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-double/src/gmxlib/scanner.l: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-double/src/gmxlib/scanner_flex.h: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-single/src/gmxlib/parser.c: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-single/src/gmxlib/parser.h: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-single/src/gmxlib/parser.y: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-single/src/gmxlib/scanner.c: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-single/src/gmxlib/scanner.l: Cannot stat: No such file or directory cpio: gromacs-4.5.5/openmpi-single/src/gmxlib/scanner_flex.h: Cannot stat: No such file or directory cpio: gromacs-4.5.5/single/src/gmxlib/parser.c: Cannot stat: No such file or directory cpio: gromacs-4.5.5/single/src/gmxlib/parser.h: Cannot stat: No such file or directory cpio: gromacs-4.5.5/single/src/gmxlib/parser.y: Cannot stat: No such file or directory cpio: gromacs-4.5.5/single/src/gmxlib/scanner.c: Cannot stat: No such file or directory cpio: gromacs-4.5.5/single/src/gmxlib/scanner.l: Cannot stat: No such file or directory cpio: gromacs-4.5.5/single/src/gmxlib/scanner_flex.h: Cannot stat: No such file or directory 24117 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump + /usr/lib/rpm/brp-python-bytecompile + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Processing files: gromacs-4.5.5-2.el6.ppc64 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libdl.so.2()(64bit) libfftw3.so.3()(64bit) libfftw3f.so.3()(64bit) libgmx.so.6()(64bit) libgmx_d.so.6()(64bit) libgmxana.so.6()(64bit) libgmxana_d.so.6()(64bit) libgmxpreprocess.so.6()(64bit) libgmxpreprocess_d.so.6()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.3)(64bit) libmd.so.6()(64bit) libmd_d.so.6()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.3)(64bit) libxml2.so.2()(64bit) rtld(GNU_HASH) Obsoletes: gromacs < 4.5.2-1 Processing files: gromacs-common-4.5.5-2.el6.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.d1ALcH + umask 022 + cd /builddir/build/BUILD + cd gromacs-4.5.5 + DOCDIR=/builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/doc/gromacs-common-4.5.5 + export DOCDIR + rm -rf /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/doc/gromacs-common-4.5.5 + /bin/mkdir -p /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/doc/gromacs-common-4.5.5 + cp -pr AUTHORS COPYING README manual-4.5.4.pdf README.fedora /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/doc/gromacs-common-4.5.5 + exit 0 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Obsoletes: gromacs-common < 4.0.7-1 Processing files: gromacs-devel-4.5.5-2.el6.ppc64 Provides: pkgconfig(libgmx) = 4.5.5 pkgconfig(libgmx_d) = 4.5.5 pkgconfig(libgmxana) = 4.5.5 pkgconfig(libgmxana_d) = 4.5.5 pkgconfig(libgmxpreprocess) = 4.5.5 pkgconfig(libgmxpreprocess_d) = 4.5.5 pkgconfig(libmd) = 4.5.5 pkgconfig(libmd_d) = 4.5.5 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Requires: /usr/bin/pkg-config libgmx.so.6()(64bit) libgmx_d.so.6()(64bit) libgmxana.so.6()(64bit) libgmxana_d.so.6()(64bit) libgmxpreprocess.so.6()(64bit) libgmxpreprocess_d.so.6()(64bit) libmd.so.6()(64bit) libmd_d.so.6()(64bit) pkgconfig(fftw3) pkgconfig(fftw3f) pkgconfig(libgmx) pkgconfig(libgmx_d) pkgconfig(libmd) pkgconfig(libmd_d) pkgconfig(libxml-2.0) Processing files: gromacs-libs-4.5.5-2.el6.ppc64 Provides: libgmx.so.6()(64bit) libgmx_d.so.6()(64bit) libgmxana.so.6()(64bit) libgmxana_d.so.6()(64bit) libgmxpreprocess.so.6()(64bit) libgmxpreprocess_d.so.6()(64bit) libmd.so.6()(64bit) libmd_d.so.6()(64bit) Requires(interp): /sbin/ldconfig /sbin/ldconfig Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /sbin/ldconfig Requires(postun): /sbin/ldconfig Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.3)(64bit) libfftw3.so.3()(64bit) libfftw3f.so.3()(64bit) libgmx.so.6()(64bit) libgmx_d.so.6()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.3)(64bit) libmd.so.6()(64bit) libmd_d.so.6()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.3)(64bit) libpthread.so.0(GLIBC_2.3.2)(64bit) libpthread.so.0(GLIBC_2.3.4)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) rtld(GNU_HASH) Processing files: gromacs-openmpi-4.5.5-2.el6.ppc64 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libdl.so.2()(64bit) libfftw3.so.3()(64bit) libfftw3f.so.3()(64bit) libgmx_openmpi.so.6()(64bit) libgmx_openmpi_d.so.6()(64bit) libgmxpreprocess_openmpi.so.6()(64bit) libgmxpreprocess_openmpi_d.so.6()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.3)(64bit) libmd_openmpi.so.6()(64bit) libmd_openmpi_d.so.6()(64bit) libmpi.so.1()(64bit) libpthread.so.0()(64bit) libxml2.so.2()(64bit) rtld(GNU_HASH) Obsoletes: gromacs-mpi < 4.5.5-2.el6 gromacs-openmpi < 4.5.3-2 Processing files: gromacs-openmpi-libs-4.5.5-2.el6.ppc64 Provides: libgmx_openmpi.so.6()(64bit) libgmx_openmpi_d.so.6()(64bit) libgmxpreprocess_openmpi.so.6()(64bit) libgmxpreprocess_openmpi_d.so.6()(64bit) libmd_openmpi.so.6()(64bit) libmd_openmpi_d.so.6()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.3)(64bit) libfftw3.so.3()(64bit) libfftw3f.so.3()(64bit) libgmx_openmpi.so.6()(64bit) libgmx_openmpi_d.so.6()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.3)(64bit) libmd_openmpi.so.6()(64bit) libmd_openmpi_d.so.6()(64bit) libmpi.so.1()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.3)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) rtld(GNU_HASH) Obsoletes: gromacs-mpi-libs < 4.5.5-2.el6 Processing files: gromacs-openmpi-devel-4.5.5-2.el6.ppc64 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Requires: libgmx_openmpi.so.6()(64bit) libgmx_openmpi_d.so.6()(64bit) libgmxpreprocess_openmpi.so.6()(64bit) libgmxpreprocess_openmpi_d.so.6()(64bit) libmd_openmpi.so.6()(64bit) libmd_openmpi_d.so.6()(64bit) Obsoletes: gromacs-mpi-devel < 4.5.5-2.el6 Processing files: gromacs-bash-4.5.5-2.el6.noarch Provides: config(gromacs-bash) = 4.5.5-2.el6 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Obsoletes: gromacs-bash < 4.0.7-1 Processing files: gromacs-zsh-4.5.5-2.el6.noarch Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Obsoletes: gromacs-zsh < 4.0.7-1 Processing files: gromacs-csh-4.5.5-2.el6.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.OflhaR + umask 022 + cd /builddir/build/BUILD + cd gromacs-4.5.5 + DOCDIR=/builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/doc/gromacs-csh-4.5.5 + export DOCDIR + rm -rf /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/doc/gromacs-csh-4.5.5 + /bin/mkdir -p /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/doc/gromacs-csh-4.5.5 + cp -pr completion.csh /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64/usr/share/doc/gromacs-csh-4.5.5 + exit 0 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Obsoletes: gromacs-csh < 4.0.7-1 Processing files: gromacs-tutor-4.5.5-2.el6.noarch Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(VersionedDependencies) <= 3.0.3-1 Obsoletes: gromacs-tutor < 4.0.7-1 Processing files: gromacs-debuginfo-4.5.5-2.el6.ppc64 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 warning: Could not canonicalize hostname: ppc12.phx2.fedoraproject.org Wrote: /builddir/build/RPMS/gromacs-4.5.5-2.el6.ppc64.rpm Wrote: /builddir/build/RPMS/gromacs-common-4.5.5-2.el6.noarch.rpm Wrote: /builddir/build/RPMS/gromacs-devel-4.5.5-2.el6.ppc64.rpm Wrote: /builddir/build/RPMS/gromacs-libs-4.5.5-2.el6.ppc64.rpm Wrote: /builddir/build/RPMS/gromacs-openmpi-4.5.5-2.el6.ppc64.rpm Wrote: /builddir/build/RPMS/gromacs-openmpi-libs-4.5.5-2.el6.ppc64.rpm Wrote: /builddir/build/RPMS/gromacs-openmpi-devel-4.5.5-2.el6.ppc64.rpm Wrote: /builddir/build/RPMS/gromacs-bash-4.5.5-2.el6.noarch.rpm Wrote: /builddir/build/RPMS/gromacs-zsh-4.5.5-2.el6.noarch.rpm Wrote: /builddir/build/RPMS/gromacs-csh-4.5.5-2.el6.noarch.rpm Wrote: /builddir/build/RPMS/gromacs-tutor-4.5.5-2.el6.noarch.rpm Wrote: /builddir/build/RPMS/gromacs-debuginfo-4.5.5-2.el6.ppc64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.FLFLsM + umask 022 + cd /builddir/build/BUILD + cd gromacs-4.5.5 + rm -rf /builddir/build/BUILDROOT/gromacs-4.5.5-2.el6.ppc64 + exit 0 Child returncode was: 0 LEAVE do -->