build.log

build.log (text/x-log), 10.79 KB, created by Juergen Rose on 2016-09-03 12:24:20 UTC

[32;01m * [39;49;00mPackage:    sci-chemistry/gromacs-2016
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail],[e-mail]
[32;01m * [39;49;00mUSE:        X abi_x86_64 amd64 cpu_flags_x86_sse2 doc elibc_glibc hwloc kernel_linux mkl mpi offensive openmp single-precision threads tng userland_GNU
[32;01m * [39;49;00mFEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking gromacs-2016.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-2016/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-2016/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016 ...
 [32;01m*[0m Configuring for float precision
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float"
cmake -C /var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=/opt/intel/*/mkl/include -DMKL_LIBRARIES=/opt/intel/*/mkl/lib/*64/libmkl_rt.so -DGMX_X11=yes -DGMX_EXTERNAL_BLAS=no -DGMX_EXTERNAL_LAPACK=no -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=yes -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=yes -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=SSE2 -DGMX_LIB_INSTALL_DIR=lib64 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DBUILD_TESTING=OFF -DGMX_BUILD_UNITTESTS=OFF -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DGMX_THREAD_MPI=yes -DGMX_GPU=OFF  -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float/gentoo_toolchain.cmake  /var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016
loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float/gentoo_common_config.cmake
Re-run cmake no build system arguments
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- 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
-- Detecting C compile features
-- Detecting C compile features - 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
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- 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_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_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
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.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 include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - 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
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for zlibVersion in /usr/lib64/libz.so
-- Looking for zlibVersion in /usr/lib64/libz.so - found
-- hwloc version: 1.11.2
-- Found Hwloc: /usr/lib64/libhwloc.so (found suitable version "1.11.2", minimum required is "1.5") 
-- 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 pthread.h
-- Looking for 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  
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- 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 pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- Performing Test C_msse2_FLAG_WORKS
-- Performing Test C_msse2_FLAG_WORKS - Success
-- Performing Test C_msse2_COMPILE_WORKS
-- Performing Test C_msse2_COMPILE_WORKS - Success
-- Performing Test CXX_msse2_FLAG_WORKS
-- Performing Test CXX_msse2_FLAG_WORKS - Success
-- Performing Test CXX_msse2_COMPILE_WORKS
-- Performing Test CXX_msse2_COMPILE_WORKS - Success
-- Enabling SSE2 SIMD instructions
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_ 
-- Performing Test _callconv_  - Success
-- Looking for DftiCreateDescriptor
-- Looking for DftiCreateDescriptor - not found
CMake Error at cmake/gmxManageFFTLibraries.cmake:154 (message):
  Linking with MKL was requested, but was not successful: The include path to
  mkl.h in MKL_INCLUDE_DIR, and the link libraries in
  MKL_LIBRARIES=/opt/intel/*/mkl/lib/*64/libmkl_rt.so need to match what the
  MKL documentation says you need for your system: Use full paths to library
  files, in the right order, and separated by semicolons.
Call Stack (most recent call first):
  CMakeLists.txt:690 (include)


-- Configuring incomplete, errors occurred!
See also "/var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float/CMakeFiles/CMakeOutput.log".
See also "/var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float/CMakeFiles/CMakeError.log".
 [31;01m*[0m ERROR: sci-chemistry/gromacs-2016::gentoo failed (configure phase):
 [31;01m*[0m   cmake failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line  115:  Called src_configure
 [31;01m*[0m   environment, line 3331:  Called cmake-utils_src_configure
 [31;01m*[0m   environment, line  955:  Called _cmake_execute_optionally 'src_configure'
 [31;01m*[0m   environment, line  446:  Called enable_cmake-utils_src_configure
 [31;01m*[0m   environment, line 1461:  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-2016::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-2016::gentoo'`.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-2016/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-2016/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float'
 [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016'