gromacs-5.0_beta1:20140323-171811.log

gromacs-5.0_beta1:20140323-171811.log (text/plain), 60.75 KB, created by Justin Lecher (RETIRED) on 2014-03-23 19:05:47 UTC

[32;01m * [39;49;00mPackage:    sci-chemistry/gromacs-5.0_beta1
[32;01m * [39;49;00mRepository: science
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail]
[32;01m * [39;49;00mUSE:        X amd64 blas cuda doc elibc_glibc fftw kernel_linux lapack offensive openmp single-precision sse2 sse4_1 threads userland_GNU
[32;01m * [39;49;00mFEATURES:   ccache compressdebug preserve-libs sandbox splitdebug userpriv usersandbox
>>> Unpacking source...
>>> Unpacking gromacs-5.0-beta1.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1 ...
 [32;01m*[0m Configuring for float precision
removed ‘/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/cmake/FindBLAS.cmake’
removed ‘/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/cmake/FindLAPACK.cmake’
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float"
cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_GSL=OFF -DGMX_EXTERNAL_LAPACK=ON -DGMX_OPENMP=ON -DGMX_COOL_QUOTES=ON -DGMX_BUILD_MANUAL=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION=SSE4.1 -DGMXLIB=lib64 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DGMX_PREFIX_LIBMD=ON -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF -DGMX_USE_GCC44_BUG_WORKAROUND=OFF -DBUILD_TESTING=OFF -DGMX_BUILD_UNITTESTS=OFF -DGMX_LIB_INSTALL_DIR=lib64 -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DGMX_THREAD_MPI=ON -DGMX_GPU=ON -DGMX_OPENMM=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-5.0_beta1/work/gromacs-5.0_beta1_float/gentoo_rules.cmake  /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1
Not searching for unused variables given on the command line.
loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/gentoo_common_config.cmake
Re-run cmake no build system arguments
-- The C compiler identification is GNU 4.8.2
-- The CXX compiler identification is GNU 4.8.2
-- Check for working C compiler using: Ninja
-- Check for working C compiler using: Ninja -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler using: Ninja
-- Check for working CXX compiler using: Ninja -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX 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 "5.5", minimum required is "3.2") 
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detecting best acceleration for this CPU
-- Detected best acceleration for this CPU - AVX_256
-- 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_EFFCXX
-- Performing Test CXXFLAGS_WARN_EFFCXX - 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
-- 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 C++ include regex
-- Looking for C++ include regex - not 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 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 clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- 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 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 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
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.1") 
-- 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 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  
-- 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
-- Performing Test CXXFLAG_FPIC
-- Performing Test CXXFLAG_FPIC - Success
-- Boost version: 1.55.0
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- Checking floating point format
-- Checking floating point format - IEEE754 (LE byte, LE word)
-- 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
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test GMX_CXX11
-- Performing Test GMX_CXX11 - Success
CMake Warning at CMakeLists.txt:701 (message):
  Please manually add compiler flags to CUDA_NVCC_FLAGS.  Automatic
  propogation temporary not working.


-- Checking for system XDR support
-- Checking for system XDR support - present
-- Performing Test GNU_AVX_CFLAG
-- Performing Test GNU_AVX_CFLAG - Success
-- Performing Test GNU_AVX_CXXFLAG
-- Performing Test GNU_AVX_CXXFLAG - Success
-- Looking for immintrin.h
-- Looking for immintrin.h - found
-- Looking for x86intrin.h
-- Looking for x86intrin.h - found
-- Looking for intrin.h
-- Looking for intrin.h - not found
-- Enabling 256-bit AVX Gromacs acceleration
-- Found PkgConfig: /usr/bin/x86_64-pc-linux-gnu-pkg-config (found version "0.28") 
-- 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 - found
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found
CMake Warning at CMakeLists.txt:989 (message):
  The FFTW library was compiled with --enable-avx to enable AVX SIMD
  instructions.  That might sound like a good idea for your processor, but
  for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD
  instructions for the way GROMACS uses FFTs.  Limitations in the way FFTW
  allows GROMACS to measure performance make it awkward for either GROMACS or
  FFTW to make the decision for you based on runtime performance.  You should
  compile a different FFTW library with --enable-sse or --enable-sse2.  If
  you have a more recent FFTW, you may like to compare the performance of
  GROMACS with FFTW libraries compiled with and without --enable-avx.
  However, the GROMACS developers do not really expect the FFTW AVX
  optimization to help, because the performance is limited by memory access,
  not computation.


-- Using external FFT library - FFTW3
-- checking for module 'blas'
--   found blas, version 3.10.1
-- Found BLAS: /usr/lib64/libf77blas.so  
-- checking for module 'lapack'
--   found lapack, version 3.10.1
-- Found LAPACK: /usr/lib64/libatllapack.so;/usr/lib64/libf77blas.so;/usr/lib64/libatlcblas.so  
-- 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).
-- Using manually set binary suffix: ""
-- Using manually set library suffix: ""
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") 
-- Found PythonInterp: /usr/bin/python (found version "2.7.6") 
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3 
C++             -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3 
Linker flags:
Executable         -Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common
Module           -Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common
Shared            -Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1 ...
 [32;01m*[0m Compiling for float precision
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float"
ninja -j12 -l9 -v
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[7/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/xmb.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/xmb.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/xmb.cpp
[8/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o -MF "src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o.d" -o src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/mdrun/membed.c
[9/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o -MF "src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o.d" -o src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/mdrun/pme_loadbal.c
[10/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o -MF "src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o.d" -o src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/mdrun/md.c
[11/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF "src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d" -o src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/mdrun/mdrun.cpp
[12/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/g_protonate.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/g_protonate.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/g_protonate.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_protonate.c
[13/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/convparm.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/convparm.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/convparm.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/convparm.c
[14/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/tpbconv.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/tpbconv.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/tpbconv.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/tpbconv.c
[15/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/gmxcheck.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/gmxcheck.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/gmxcheck.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/gmxcheck.c
[16/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/specbond.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/specbond.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/specbond.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/specbond.c
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp: In function ‘t_fgrid* FGridFromFile(const char*)’:
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp:378:27: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(in, "%6s", buf);
                           ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp:391:28: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(in, "%15s", buf);
                            ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp:412:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
             fscanf(in, "%15s", buf);
                                    ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp:416:40: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
                 fscanf(in, "%15s", buf);
                                        ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp:435:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
             fscanf(in, "%15s", buf);
                                    ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp:439:32: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
         fscanf(in, "%15s", buf);
                                ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp: In function ‘void ReadAccOpen(const char*, FILE*)’:
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp:106:27: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(in, "%4s", buf);
                           ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp: In function ‘void ReadAccClose(const char*, FILE*)’:
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/fgrid.cpp:117:27: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(in, "%4s", buf);
                           ^
[17/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/gmxdump.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/gmxdump.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/gmxdump.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/gmxdump.c
[18/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/xlate.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/xlate.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/xlate.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/xlate.c
[19/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/g_x2top.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/g_x2top.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/g_x2top.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_x2top.c
[20/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/tomorse.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/tomorse.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/tomorse.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/tomorse.c
[21/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/tpbcmp.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/tpbcmp.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/tpbcmp.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/tpbcmp.c
[22/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/grompp.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/grompp.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/grompp.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c
[23/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/hizzie.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/hizzie.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/hizzie.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/hizzie.c
[24/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/pdb2gmx.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/pdb2gmx.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/pdb2gmx.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/pdb2gmx.c
[25/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc  -DHAVE_CONFIG_H  -DNDEBUG -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wunused-parameter   -g -march=native -mtune=native -Wimplicit-function-declaration -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx/nm2type.c.o -MF "src/programs/CMakeFiles/gmx_objlib.dir/gmx/nm2type.c.o.d" -o src/programs/CMakeFiles/gmx_objlib.dir/gmx/nm2type.c.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/nm2type.c
[26/825] cd /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_copyrite_gpu.cu.o.cmake
[27/825] cd /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/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-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_pmalloc_cuda.cu.o.cmake
[28/825] cd /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/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-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.cmake
[29/825] cd /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/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-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_memtestG80_core.cu.o.cmake
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_x2top.c: In function ‘lo_set_force_const’:
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_x2top.c:270:30: warning: array subscript is above array bounds [-Warray-bounds]
             plist->param[i].c[nrfp+j] = c[j];
                              ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_x2top.c:270:30: warning: array subscript is above array bounds [-Warray-bounds]
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_x2top.c:270:30: warning: array subscript is above array bounds [-Warray-bounds]
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_x2top.c:270:30: warning: array subscript is above array bounds [-Warray-bounds]
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_x2top.c:270:30: warning: array subscript is above array bounds [-Warray-bounds]
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/g_x2top.c:270:30: warning: array subscript is above array bounds [-Warray-bounds]
[30/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/xutil.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/xutil.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/xutil.cpp
[31/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/molps.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/molps.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/molps.cpp
[32/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/xdlghi.cpp
[33/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/logo.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/logo.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/logo.cpp
[34/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/xdlg.cpp
[35/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/nmol.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/nmol.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/nmol.cpp
[36/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/filter.cpp
[37/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/buttons.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/buttons.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/buttons.cpp
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c: In function ‘gmx_grompp’:
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c:902:51: warning: array subscript is above array bounds [-Warray-bounds]
                                 xp[i][j] += invbox[k][j]*xp[i][k];
                                                   ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c:923:37: warning: array subscript is above array bounds [-Warray-bounds]
                     com[j] += invbox[k][j]*com[k];
                                     ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c:902:51: warning: array subscript is above array bounds [-Warray-bounds]
                                 xp[i][j] += invbox[k][j]*xp[i][k];
                                                   ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c:923:37: warning: array subscript is above array bounds [-Warray-bounds]
                     com[j] += invbox[k][j]*com[k];
                                     ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c:902:51: warning: array subscript is above array bounds [-Warray-bounds]
                                 xp[i][j] += invbox[k][j]*xp[i][k];
                                                   ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c:923:37: warning: array subscript is above array bounds [-Warray-bounds]
                     com[j] += invbox[k][j]*com[k];
                                     ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c:902:51: warning: array subscript is above array bounds [-Warray-bounds]
                                 xp[i][j] += invbox[k][j]*xp[i][k];
                                                   ^
/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/gmx/grompp.c:923:37: warning: array subscript is above array bounds [-Warray-bounds]
                     com[j] += invbox[k][j]*com[k];
                                     ^
[38/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/pulldown.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/pulldown.cpp
[39/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/nleg.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/nleg.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/nleg.cpp
[40/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/xdlgitem.cpp
[41/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/view.cpp
[42/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/popup.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/popup.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/popup.cpp
[43/825] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++  -DHAVE_CONFIG_H  -DNDEBUG -mavx   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused-function   -g -march=native -mtune=native -Wenum-compare -O3  -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src -Isrc -Isrc/gromacs/utility -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/legacyheaders -I/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/gromacs/gmxpreprocess -MMD -MT src/programs/CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -MF "src/programs/CMakeFiles/view_objlib.dir/view/dialogs.cpp.o.d" -o src/programs/CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1/src/programs/view/dialogs.cpp
FAILED: cd /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_cudautils.cu.o.cmake
/usr/include/boost/assert.hpp:102:47: error: ‘noinline’ was not declared in this scope
           BOOST_NOINLINE void assertion_failed_msg(CharT const * expr, char const * msg, char const * function,
                                               ^
CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:261 (message):
  Error generating file
  /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o


FAILED: cd /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/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-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.cmake
/usr/include/boost/assert.hpp:102:47: error: ‘noinline’ was not declared in this scope
           BOOST_NOINLINE void assertion_failed_msg(CharT const * expr, char const * msg, char const * function,
                                               ^
CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:261 (message):
  Error generating file
  /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


ninja: build stopped: subcommand failed.
 [31;01m*[0m ERROR: sci-chemistry/gromacs-5.0_beta1::science failed (compile phase):
 [31;01m*[0m   (no error message)
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line   93:  Called src_compile
 [31;01m*[0m   environment, line 3137:  Called cmake-utils_src_compile
 [31;01m*[0m   environment, line  874:  Called _execute_optionaly 'src_compile'
 [31;01m*[0m   environment, line  445:  Called enable_cmake-utils_src_compile
 [31;01m*[0m   environment, line 1142:  Called cmake-utils_src_make
 [31;01m*[0m   environment, line  889:  Called ninja_src_make
 [31;01m*[0m   environment, line 2678:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       "$@" || die
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-chemistry/gromacs-5.0_beta1::science'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-5.0_beta1::science'`.
 [31;01m*[0m The complete build log is located at '/var/log/portage/build/sci-chemistry/gromacs-5.0_beta1:20140323-171811.log'.
 [31;01m*[0m For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float'
 [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0-beta1'