* Package: sci-chemistry/gromacs-4.5.4-r2  * Repository: gentoo  * Maintainer: sci-chemistry@gentoo.org  * USE: X amd64 bash-completion blas doc elibc_glibc fftw gsl kernel_linux lapack mpi multilib single-precision sse2 threads userland_GNU xml  * FEATURES: sandbox >>> Unpacking source... >>> Unpacking gromacs-4.5.4.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work >>> Unpacking 0001-Make-stack-non-executable-for-GAS-assembly.patch.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work >>> Unpacking 0002-Make-stack-non-executable-for-ATT-assembly.patch.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work >>> Unpacking gromacs-manual-4.5.4.pdf to /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work unpack gromacs-manual-4.5.4.pdf: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work >>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work/gromacs-4.5.4 ... * mdrun uses only threads OR mpi, and gromacs favours the * use of mpi over threads, so a mpi-version of mdrun will * be compiled. If you want to run mdrun on shared memory * machines only, you can safely disable mpi * Applying 0001-Make-stack-non-executable-for-GAS-assembly.patch ...  [ ok ] * Applying 0002-Make-stack-non-executable-for-ATT-assembly.patch ...  [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work/gromacs-4.5.4 ... * You have enabled mpi, only mdrun will make use of mpi, that is why * we configure/compile gromacs twice (with and without mpi) and only * install mdrun with mpi support. In addtion you will get libgmx and * libmd with and without mpi support. * Configuring for float precision >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work/gromacs-4.5.4_float" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/temp/gentoo_common_config.cmake -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_GSL=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_THREADS=ON -DGMX_XML=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION=sse -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -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-4.5.4-r2/temp/gentoo_rules.cmake /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work/gromacs-4.5.4 Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/temp/gentoo_common_config.cmake Re-run cmake no build system arguments -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- 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 -- 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 -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - 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_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 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 - found -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - found -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include files HAVE_PMMINTRIN_H - found -- Looking for include files HAVE_SMMINTRIN_H -- Looking for include files HAVE_SMMINTRIN_H - 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 - little endian -- checking for module 'libxml-2.0' -- found libxml-2.0, version 2.7.8 -- Found LibXml2: /usr/lib64/libxml2.so -- 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 -- 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 -- 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 -- The Fortran compiler identification is GNU -- Check for working Fortran compiler: /usr/bin/gfortran -- Check for working Fortran compiler: /usr/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes CMake Error at cmake/FindBLAS.cmake:457 (message): A required library with BLAS API not found. Please specify library location. Call Stack (most recent call first): CMakeLists.txt:739 (find_package) -- Configuring incomplete, errors occurred! * ERROR: sci-chemistry/gromacs-4.5.4-r2 failed (configure phase): * cmake failed * * Call stack: * ebuild.sh, line 56: Called src_configure * environment, line 3185: Called cmake-utils_src_configure * environment, line 992: Called _execute_optionaly 'src_configure' * environment, line 393: Called enable_cmake-utils_src_configure * environment, line 1318: Called die * The specific snippet of code: * "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed"; * * If you need support, post the output of 'emerge --info =sci-chemistry/gromacs-4.5.4-r2', * the complete build log and the output of 'emerge -pqv =sci-chemistry/gromacs-4.5.4-r2'. * The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/temp/environment'. * S: '/var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work/gromacs-4.5.4'