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Gentoo's Bugzilla – Attachment 299563 Details for
Bug 399755
dev-util/cmake: pkg-config library path not respected by cmake in Find_{BLAS,LAPACK}.cmake
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build.log
build.log (text/plain), 43.07 KB, created by
Aleksandr Yakimov
on 2012-01-22 18:48:52 UTC
(
hide
)
Description:
build.log
Filename:
MIME Type:
Creator:
Aleksandr Yakimov
Created:
2012-01-22 18:48:52 UTC
Size:
43.07 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-chemistry/gromacs-4.5.5-r1 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: sci-chemistry@gentoo.org >[32;01m * [39;49;00mUSE: X amd64 blas consolekit double-precision elibc_glibc fftw kernel_linux lapack multilib policykit sse2 threads userland_GNU xml >[32;01m * [39;49;00mFEATURES: preserve-libs sandbox >>>> Unpacking source... >>>> Unpacking gromacs-4.5.5.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work >>>> Unpacking 0001-Make-stack-non-executable-for-GAS-assembly.patch.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work >>>> Unpacking 0002-Make-stack-non-executable-for-ATT-assembly.patch.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5 ... > [32;01m*[0m Applying 0001-Make-stack-non-executable-for-GAS-assembly.patch ... >[A[72C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying 0002-Make-stack-non-executable-for-ATT-assembly.patch ... >[A[72C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying gromacs-4.5.5-cmake-cpp-asm.patch ... >[A[72C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying gromacs-4.5.5-enable-see.patch ... >[A[72C [34;01m[ [32;01mok[34;01m ][0m >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5 ... > [32;01m*[0m > [32;01m*[0m For most simulations single precision is accurate enough. In some > [32;01m*[0m cases double precision is required to get reasonable results: > [32;01m*[0m > [32;01m*[0m -normal mode analysis, for the conjugate gradient or l-bfgs minimization > [32;01m*[0m and the calculation and diagonalization of the Hessian > [32;01m*[0m -calculation of the constraint force between two large groups of atoms > [32;01m*[0m -energy conservation: this can only be done without temperature coupling and > [32;01m*[0m without cutoffs > [32;01m*[0m > [32;01m*[0m Configuring for double precision >ÑдалÑн «/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/cmake/FindBLAS.cmake» >ÑдалÑн «/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/cmake/FindLAPACK.cmake» >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5_double" >cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/gentoo_common_config.cmake -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_GSL=OFF -DGMX_EXTERNAL_LAPACK=ON -DGMX_THREADS=ON -DGMX_XML=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION=sse -DGMXLIB=lib64 -DGMX_DOUBLE=ON -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-4.5.5-r1/temp/gentoo_rules.cmake /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5 >Not searching for unused variables given on the command line. >loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/gentoo_common_config.cmake >-- 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 >-- 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 >-- 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 FFTW3: /usr/lib64/libfftw3.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 >-- checking for module 'blas' >-- found blas, version 5.1.0 >-- checking for module 'lapack' >-- found lapack, version 5.1.0 >-- The ASM-ATT compiler identification is GNU >-- Found assembler: /usr/bin/as >-- <<< Gentoo configuration >>> >Build type Gentoo >Install path /usr >Compiler flags: >C -O2 -pipe -march=native -mtune=native >C++ -O2 -pipe -march=native -mtune=native >Linker flags: >Executable -Wl,-O1 -Wl,--as-needed,--hash-style=gnu,--sort-common >Module -Wl,-O1 -Wl,--as-needed,--hash-style=gnu,--sort-common >Shared -Wl,-O1 -Wl,--as-needed,--hash-style=gnu,--sort-common > >-- Configuring done >-- Generating done >-- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5_double >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5 ... > [32;01m*[0m Compiling for double precision >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5_double" >make -j17 >[35m[1mScanning dependencies of target gmx >[0m[ 0%] [ 0%] [ 0%] [ 0%] [ 0%] [ 1%] [ 1%] [ 1%] [ 1%] [32mBuilding C object src/gmxlib/CMakeFiles/gmx.dir/warninp.c.o >[0m[32mBuilding C object src/gmxlib/CMakeFiles/gmx.dir/gmx_system_xdr.c.o >[0m[32mBuilding C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o >[0m[32mBuilding C object src/gmxlib/CMakeFiles/gmx.dir/orires.c.o >[32mBuilding C 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>/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/comm.c:428:42: замеÑание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6 >[32mBuilding C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/topology.c.o >[0m[ 43%] /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/scatter.c: Ð ÑÑнкÑии «tMPI_Scatter»: >/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/scatter.c:70:25: замеÑание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6 >/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/gather.c: Ð ÑÑнкÑии «tMPI_Gather»: >/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/gather.c:69:25: замеÑание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6 >[32mBuilding C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/list.c.o >[0m[ 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>[0m/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/topology.c: Ð ÑÑнкÑии «tMPI_Cart_get»: >/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/topology.c:105:42: замеÑание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6 >/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/once.c: Ð ÑÑнкÑии «tMPI_Once»: >/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/once.c:75:38: замеÑание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6 >[31m[1mLinking C shared library libgmx.so >[0m/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lacml >/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lacml >collect2: вÑполнение ld завеÑÑилоÑÑ Ñ ÐºÐ¾Ð´Ð¾Ð¼ возвÑаÑа 1 >make[2]: *** [src/gmxlib/libgmx.so.6] ÐÑибка 1 >make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] ÐÑибка 2 >make: *** [all] ÐÑибка 2 > [31;01m*[0m ERROR: sci-chemistry/gromacs-4.5.5-r1 failed (compile phase): > [31;01m*[0m emake failed > [31;01m*[0m > [31;01m*[0m If you need support, post the output of 'emerge --info =sci-chemistry/gromacs-4.5.5-r1', > [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-chemistry/gromacs-4.5.5-r1'. > [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/build.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/environment'. > [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5'
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