/var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/temp/build.log

build.log (text/plain), 11.89 KB, created by Juergen Rose on 2011-06-30 09:40:11 UTC

[32;01m * [39;49;00mPackage:    sci-chemistry/gromacs-4.5.4-r2
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        X amd64 bash-completion blas doc elibc_glibc fftw gsl kernel_linux lapack mpi multilib single-precision sse2 threads userland_GNU xml
[32;01m * [39;49;00mFEATURES:   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 ...
 [32;01m*[0m mdrun uses only threads OR mpi, and gromacs favours the
 [32;01m*[0m use of mpi over threads, so a mpi-version of mdrun will
 [32;01m*[0m be compiled. If you want to run mdrun on shared memory
 [32;01m*[0m machines only, you can safely disable mpi
 [32;01m*[0m Applying 0001-Make-stack-non-executable-for-GAS-assembly.patch ...
[A[166C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying 0002-Make-stack-non-executable-for-ATT-assembly.patch ...
[A[166C [34;01m[ [32;01mok[34;01m ][0m
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work/gromacs-4.5.4 ...
 [32;01m*[0m You have enabled mpi, only mdrun will make use of mpi, that is why
 [32;01m*[0m we configure/compile gromacs twice (with and without mpi) and only
 [32;01m*[0m install mdrun with mpi support. In addtion you will get libgmx and
 [32;01m*[0m libmd with and without mpi support.
 [32;01m*[0m 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!
 [31;01m*[0m ERROR: sci-chemistry/gromacs-4.5.4-r2 failed (configure phase):
 [31;01m*[0m   cmake failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line   56:  Called src_configure
 [31;01m*[0m   environment, line 3185:  Called cmake-utils_src_configure
 [31;01m*[0m   environment, line  992:  Called _execute_optionaly 'src_configure'
 [31;01m*[0m   environment, line  393:  Called enable_cmake-utils_src_configure
 [31;01m*[0m   environment, line 1318:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed";
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-chemistry/gromacs-4.5.4-r2',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-chemistry/gromacs-4.5.4-r2'.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/gromacs-4.5.4-r2/work/gromacs-4.5.4'