* Package: sci-chemistry/gromacs-4.6_beta1  * Repository: gentoo  * Maintainer: ottxor@gentoo.org sci-chemistry@gentoo.org  * USE: X amd64 blas cuda doc elibc_glibc fftw gsl kernel_linux lapack mpi openmp single-precision sse2 threads userland_GNU  * FEATURES: sandbox splitdebug >>> Unpacking source... >>> Unpacking gromacs-4.6-beta1.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work >>> Unpacking gromacs-manual-4.6-beta1.pdf to /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work unpack gromacs-manual-4.6-beta1.pdf: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1 ... * Configuring for float precision removed '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/cmake/FindBLAS.cmake' removed '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/cmake/FindLAPACK.cmake' >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_GSL=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_OPENMP=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION=SSE2 -DGMXLIB=lib64 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DGMX_THREAD_MPI=ON -DGMX_GPU=ON -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/gentoo_rules.cmake /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1 Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/gentoo_common_config.cmake Re-run cmake no build system arguments -- The C compiler identification is GNU 4.6.3 -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Looking for NVIDIA GPUs present in the system -- Number of NVIDIA GPUs detected: 1 -- Found CUDA: /opt/cuda (found suitable version "5.0", minimum required is "3.2") -- The CXX compiler identification is GNU 4.6.3 -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detecting best acceleration for this CPU -- Detecting best acceleration for this CPU - SSE2 -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_WARN_EXTRA -- Performing Test CFLAGS_WARN_EXTRA - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- 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_WARN_EXTRA -- Performing Test CXXFLAGS_WARN_EXTRA - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- 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: "" -- Looking for include file string.h -- Looking for include file string.h - found -- Looking for include file math.h -- Looking for include file math.h - found -- Looking for include file limits.h -- Looking for include file limits.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file direct.h -- Looking for include file direct.h - not found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file stdlib.h -- Looking for include file stdlib.h - found -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for include files rpc/rpc.h, rpc/xdr.h -- Looking for include files rpc/rpc.h, rpc/xdr.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - 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 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 sigaction -- Looking for sigaction - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for sched_setaffinity -- Looking for sched_setaffinity - found -- Looking for sched_getaffinity -- Looking for sched_getaffinity - found -- Looking for rsqrt -- Looking for rsqrt - not found -- Looking for rsqrtf -- Looking for rsqrtf - not found -- Looking for sqrtf -- Looking for sqrtf - 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 - little endian -- GSL using gsl-config /usr/bin/gsl-config -- Using GSL from /usr -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found X11: /usr/lib64/libX11.so -- Atomics found -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not 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 -- Setting the nvcc host compiler to: /usr/bin/x86_64-pc-linux-gnu-gcc -- Performing Test CXXFLAG_FPIC -- Performing Test CXXFLAG_FPIC - Success -- Setting build user/date/host/cpu information -- 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 SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for inline keyword -- Checking for inline keyword - __inline__ -- Checking for restrict keyword -- Checking for restrict keyword - __restrict__ -- Checking for pipe support -- Checking for isfinite -- Performing Test isfinite_compile_ok -- Performing Test isfinite_compile_ok - Success -- Checking for isfinite - yes -- Checking for _isfinite -- Performing Test _isfinite_compile_ok -- Performing Test _isfinite_compile_ok - Failed -- Checking for _isfinite - no -- Checking for _finite -- Performing Test _finite_compile_ok -- Performing Test _finite_compile_ok - Failed -- Checking for _finite - no -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test GNU_SSE2_CFLAG -- Performing Test GNU_SSE2_CFLAG - Success -- Performing Test GNU_SSE2_CXXFLAG -- Performing Test GNU_SSE2_CXXFLAG - Success -- Looking for emmintrin.h -- Looking for emmintrin.h - found -- Enabling SSE2 Gromacs acceleration, and it will help compiler optimization. -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") -- checking for module 'fftw3f' -- found fftw3f, version 3.3.3 -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib64/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found -- checking for module 'blas' -- found blas, version 3.10.0 -- checking for module 'lapack' -- found lapack, version 3.10.0 -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats). -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -msse2 -march=amdfam10 -O2 -g C++ -msse2 -march=amdfam10 -O2 -g Linker flags: Executable -Wl,-O1 -Wl,--as-needed Module -Wl,-O1 -Wl,--as-needed Shared -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float * Configuring for float precision with mpi >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_GSL=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_OPENMP=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION=SSE2 -DGMXLIB=lib64 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DGMX_DOUBLE=OFF -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_BINARY_SUFFIX=_mpi -DGMX_LIBS_SUFFIX=_mpi -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi/gentoo_rules.cmake /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1 Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi/gentoo_common_config.cmake Re-run cmake no build system arguments -- The C compiler identification is GNU 4.6.3 -- Check for working C compiler: /usr/bin/mpicc -- Check for working C compiler: /usr/bin/mpicc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Looking for NVIDIA GPUs present in the system -- Number of NVIDIA GPUs detected: 1 -- Found CUDA: /opt/cuda (found suitable version "5.0", minimum required is "3.2") -- The CXX compiler identification is GNU 4.6.3 -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detecting best acceleration for this CPU -- Detecting best acceleration for this CPU - SSE2 -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_WARN_EXTRA -- Performing Test CFLAGS_WARN_EXTRA - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- 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_WARN_EXTRA -- Performing Test CXXFLAGS_WARN_EXTRA - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Using manually set binary suffix: "_mpi" -- Using manually set library suffix: "_mpi" -- 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 file string.h -- Looking for include file string.h - found -- Looking for include file math.h -- Looking for include file math.h - found -- Looking for include file limits.h -- Looking for include file limits.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file direct.h -- Looking for include file direct.h - not found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file stdlib.h -- Looking for include file stdlib.h - found -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for include files rpc/rpc.h, rpc/xdr.h -- Looking for include files rpc/rpc.h, rpc/xdr.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - 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 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 sigaction -- Looking for sigaction - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for sched_setaffinity -- Looking for sched_setaffinity - found -- Looking for sched_getaffinity -- Looking for sched_getaffinity - found -- Looking for rsqrt -- Looking for rsqrt - not found -- Looking for rsqrtf -- Looking for rsqrtf - not found -- Looking for sqrtf -- Looking for sqrtf - 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 - little endian -- GSL using gsl-config /usr/bin/gsl-config -- Using GSL from /usr -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found X11: /usr/lib64/libX11.so -- Atomics found -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success CMake Warning at cmake/gmxManageNvccConfig.cmake:75 (message): Will not set the nvcc host compiler because the current C compiler is an MPI compiler wrapper: /usr/bin/mpicc MPI compiler wrappers are prone to not work with nvcc. You might get lucky, but the safest is to use the C compiler that the MPI compiler wrapper uses (if this is compatible). To manually set the nvcc host compiler, edit CUDA_NVCC_FLAGS or re-configure setting CUDA_NVCC_HOST_COMPILER to the full path of a compatible compiler. Call Stack (most recent call first): cmake/gmxManageGPU.cmake:143 (include) CMakeLists.txt:590 (gmx_gpu_setup) -- Performing Test CXXFLAG_FPIC -- Performing Test CXXFLAG_FPIC - Success -- Setting build user/date/host/cpu information -- 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 SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for inline keyword -- Checking for inline keyword - __inline__ -- Checking for restrict keyword -- Checking for restrict keyword - __restrict__ -- Checking for pipe support -- Checking for isfinite -- Performing Test isfinite_compile_ok -- Performing Test isfinite_compile_ok - Success -- Checking for isfinite - yes -- Checking for _isfinite -- Performing Test _isfinite_compile_ok -- Performing Test _isfinite_compile_ok - Failed -- Checking for _isfinite - no -- Checking for _finite -- Performing Test _finite_compile_ok -- Performing Test _finite_compile_ok - Failed -- Checking for _finite - no -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test GNU_SSE2_CFLAG -- Performing Test GNU_SSE2_CFLAG - Success -- Performing Test GNU_SSE2_CXXFLAG -- Performing Test GNU_SSE2_CXXFLAG - Success -- Looking for emmintrin.h -- Looking for emmintrin.h - found -- Enabling SSE2 Gromacs acceleration, and it will help compiler optimization. -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") -- checking for module 'fftw3f' -- found fftw3f, version 3.3.3 -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib64/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found -- checking for module 'blas' -- found blas, version 3.10.0 -- checking for module 'lapack' -- found lapack, version 3.10.0 -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats). -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -msse2 -march=amdfam10 -O2 -g C++ -msse2 -march=amdfam10 -O2 -g Linker flags: Executable -Wl,-O1 -Wl,--as-needed Module -Wl,-O1 -Wl,--as-needed Shared -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1 ... * Compiling for float precision >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float" make -j5 VERBOSE=1 /usr/bin/cmake -H/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1 -B/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/CMakeFiles /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' make -f src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/build.make src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/depend make -f src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/build.make src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/depend make -f src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/build.make src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/depend make[2]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/CMakeFiles /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/CMakeFiles [ 0%] make[2]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/CMakeFiles 97 make[2]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/CMakeFiles /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/CMakeFiles [ 0%] [ 1%] [ 1%] [ 1%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//. Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//. Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//. Building NVCC (Device) object src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o Building NVCC (Device) object src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda.cu.o cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//. cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//. cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_cudautils.cu.o.cmake cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_memtestG80_core.cu.o.cmake cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_pmalloc_cuda.cu.o.cmake -- Removing /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.cmake /usr/bin/cmake -E remove /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//nbnxn_cuda_generated_nbnxn_cuda.cu.o.cmake -- Removing /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o -- Removing /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o /usr/bin/cmake -E remove /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o -- Removing /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda.cu.o /usr/bin/cmake -E remove /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o -- Removing /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o -- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_cudautils.cu.o.NVCC-depend /usr/bin/cmake -E remove /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o -- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_pmalloc_cuda.cu.o.NVCC-depend /opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/cuda_tools/cudautils.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_cudautils.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DNVCC -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib -I/opt/cuda/include /usr/bin/cmake -E remove /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda.cu.o -- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_memtestG80_core.cu.o.NVCC-depend nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o] Error 1 make[2]: /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/CMakeFiles *** Waiting for unfinished jobs.... [ 1%] -- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.NVCC-depend Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//. /opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/cuda_tools/pmalloc_cuda.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_pmalloc_cuda.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DNVCC -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib -I/opt/cuda/include /opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DNVCC -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/mdlib/nbnxn_cuda -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/opt/cuda/include nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o /opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/gpu_utils/memtestG80_core.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_memtestG80_core.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DLINUX -DNVCC -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/gpu_utils -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/vamake[2]: r/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib -I/opt/cuda/include *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' -- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//nbnxn_cuda_generated_nbnxn_cuda.cu.o.NVCC-depend make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o make[2]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o] Error 1 make[2]: *** Waiting for unfinished jobs.... nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_memtestG80_core.cu.o] Error 1 make[2]: *** Waiting for unfinished jobs.... cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.cmake /opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/mdlib/nbnxn_cuda/nbnxn_cuda.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//nbnxn_cuda_generated_nbnxn_cuda.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DNVCC -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/mdlib/nbnxn_cuda -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/opt/cuda/include nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at nbnxn_cuda_generated_nbnxn_cuda.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda.cu.o make[2]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/./nbnxn_cuda_generated_nbnxn_cuda.cu.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' make[1]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/all] Error 2 -- Removing /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o /usr/bin/cmake -E remove /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o -- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.NVCC-depend /opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/gpu_utils/gpu_utils.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DLINUX -DNVCC -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/gpu_utils -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib -I/opt/cuda/include nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' make: *** [all] Error 2 * ERROR: sci-chemistry/gromacs-4.6_beta1 failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-chemistry/gromacs-4.6_beta1'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-4.6_beta1'`. * The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' * S: '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1'