/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/temp/build.log

build.log (text/plain), 47.01 KB, created by Juergen Rose on 2012-12-01 14:54:01 UTC

[32;01m * [39;49;00mPackage:    sci-chemistry/gromacs-4.6_beta1
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail]
[32;01m * [39;49;00mUSE:        X amd64 blas cuda doc elibc_glibc fftw gsl kernel_linux lapack mpi openmp single-precision sse2 threads userland_GNU
[32;01m * [39;49;00mFEATURES:   sandbox splitdebug
>>> Unpacking source...
>>> Unpacking gromacs-4.6-beta1.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work
>>> Unpacking gromacs-manual-4.6-beta1.pdf to /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work
unpack gromacs-manual-4.6-beta1.pdf: file format not recognized. Ignoring.
>>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1 ...
 [32;01m*[0m Configuring for float precision
removed '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/cmake/FindBLAS.cmake'
removed '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/cmake/FindLAPACK.cmake'
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float"
cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_GSL=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_OPENMP=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION=SSE2 -DGMXLIB=lib64 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DGMX_THREAD_MPI=ON -DGMX_GPU=ON -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-4.6_beta1/work/gromacs-4.6_beta1_float/gentoo_rules.cmake  /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1
Not searching for unused variables given on the command line.
loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/gentoo_common_config.cmake
Re-run cmake no build system arguments
-- The C compiler identification is GNU 4.6.3
-- 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
-- Looking for NVIDIA GPUs present in the system
-- Number of NVIDIA GPUs detected: 1 
-- Found CUDA: /opt/cuda (found suitable version "5.0", minimum required is "3.2") 
-- The CXX compiler identification is GNU 4.6.3
-- 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
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detecting best acceleration for this CPU
-- Detecting best acceleration for this CPU - SSE2
-- 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_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
-- Using manually set binary suffix: ""
-- Using manually set library suffix: ""
-- Looking for include file string.h
-- Looking for include file string.h - found
-- Looking for include file math.h
-- Looking for include file math.h - found
-- Looking for include file limits.h
-- Looking for include file limits.h - found
-- Looking for include file memory.h
-- Looking for include file memory.h - found
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file direct.h
-- Looking for include file direct.h - not found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file stdint.h
-- Looking for include file stdint.h - found
-- Looking for include file stdlib.h
-- Looking for include file stdlib.h - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file inttypes.h
-- Looking for include file inttypes.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file sys/stat.h
-- Looking for include file sys/stat.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file rpc/rpc.h
-- Looking for include file rpc/rpc.h - found
-- Looking for include files rpc/rpc.h, rpc/xdr.h
-- Looking for include files rpc/rpc.h, rpc/xdr.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 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 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 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
-- 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
-- Atomics found
-- 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  
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Setting the nvcc host compiler to: /usr/bin/x86_64-pc-linux-gnu-gcc
-- Performing Test CXXFLAG_FPIC
-- Performing Test CXXFLAG_FPIC - Success
-- Setting build user/date/host/cpu information
-- 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 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
-- Checking for system XDR support
-- Checking for system XDR support - present
-- Performing Test GNU_SSE2_CFLAG
-- Performing Test GNU_SSE2_CFLAG - Success
-- Performing Test GNU_SSE2_CXXFLAG
-- Performing Test GNU_SSE2_CXXFLAG - Success
-- Looking for emmintrin.h
-- Looking for emmintrin.h - found
-- Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") 
-- 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 - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found
-- checking for module 'blas'
--   found blas, version 3.10.0
-- checking for module 'lapack'
--   found lapack, version 3.10.0
-- 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).
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -msse2  -march=amdfam10 -O2 -g 
C++             -msse2  -march=amdfam10 -O2 -g 
Linker flags:
Executable        -Wl,-O1 -Wl,--as-needed
Module           -Wl,-O1 -Wl,--as-needed
Shared            -Wl,-O1 -Wl,--as-needed

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float
 [32;01m*[0m Configuring for float precision with mpi
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi"
cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_GSL=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_OPENMP=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION=SSE2 -DGMXLIB=lib64 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DGMX_DOUBLE=OFF -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_BINARY_SUFFIX=_mpi -DGMX_LIBS_SUFFIX=_mpi -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi/gentoo_rules.cmake  /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1
Not searching for unused variables given on the command line.
loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi/gentoo_common_config.cmake
Re-run cmake no build system arguments
-- The C compiler identification is GNU 4.6.3
-- Check for working C compiler: /usr/bin/mpicc
-- Check for working C compiler: /usr/bin/mpicc -- works
-- Detecting C compiler ABI info
-- Detecting C 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 "5.0", minimum required is "3.2") 
-- The CXX compiler identification is GNU 4.6.3
-- 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
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detecting best acceleration for this CPU
-- Detecting best acceleration for this CPU - SSE2
-- 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_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
-- Using manually set binary suffix: "_mpi"
-- Using manually set library suffix: "_mpi"
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Checking for CRAY XT Catamount compile
-- Checking for CRAY XT Catamount target - no
-- Looking for include file string.h
-- Looking for include file string.h - found
-- Looking for include file math.h
-- Looking for include file math.h - found
-- Looking for include file limits.h
-- Looking for include file limits.h - found
-- Looking for include file memory.h
-- Looking for include file memory.h - found
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file direct.h
-- Looking for include file direct.h - not found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file stdint.h
-- Looking for include file stdint.h - found
-- Looking for include file stdlib.h
-- Looking for include file stdlib.h - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file inttypes.h
-- Looking for include file inttypes.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file sys/stat.h
-- Looking for include file sys/stat.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file rpc/rpc.h
-- Looking for include file rpc/rpc.h - found
-- Looking for include files rpc/rpc.h, rpc/xdr.h
-- Looking for include files rpc/rpc.h, rpc/xdr.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 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 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 - 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
-- 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
-- Atomics found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
CMake Warning at cmake/gmxManageNvccConfig.cmake:75 (message):
  

              Will not set the nvcc host compiler because the current C compiler is an MPI
              compiler wrapper: /usr/bin/mpicc
              MPI compiler wrappers are prone to not work with nvcc. You might get lucky,
              but the safest is to use the C compiler that the MPI compiler wrapper uses
              (if this is compatible).
              To manually set the nvcc host compiler, edit CUDA_NVCC_FLAGS or re-configure
              setting CUDA_NVCC_HOST_COMPILER to the full path of a compatible compiler.
              
Call Stack (most recent call first):
  cmake/gmxManageGPU.cmake:143 (include)
  CMakeLists.txt:590 (gmx_gpu_setup)


-- Performing Test CXXFLAG_FPIC
-- Performing Test CXXFLAG_FPIC - Success
-- Setting build user/date/host/cpu information
-- 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 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
-- Checking for system XDR support
-- Checking for system XDR support - present
-- Performing Test GNU_SSE2_CFLAG
-- Performing Test GNU_SSE2_CFLAG - Success
-- Performing Test GNU_SSE2_CXXFLAG
-- Performing Test GNU_SSE2_CXXFLAG - Success
-- Looking for emmintrin.h
-- Looking for emmintrin.h - found
-- Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") 
-- 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 - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found
-- checking for module 'blas'
--   found blas, version 3.10.0
-- checking for module 'lapack'
--   found lapack, version 3.10.0
-- 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).
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
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-- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float_mpi
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[34m[1mBuilding NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
[0mcd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//.
/opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/cuda_tools/pmalloc_cuda.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_pmalloc_cuda.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DNVCC -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib -I/opt/cuda/include
/opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DNVCC -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/mdlib/nbnxn_cuda -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/opt/cuda/include
nvcc fatal   : redefinition of argument 'compiler-bindir'
CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:208 (message):
  Error generating
  /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o


/opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/gpu_utils/memtestG80_core.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_memtestG80_core.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DLINUX -DNVCC -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/gpu_utils -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/vamake[2]: r/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib -I/opt/cuda/include
*** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1
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CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:208 (message):
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cd /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/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-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.cmake
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nvcc fatal   : redefinition of argument 'compiler-bindir'
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  Error generating
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-- Removing /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
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-- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.NVCC-depend
/opt/cuda/bin/nvcc -M -D__CUDACC__ /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/gpu_utils/gpu_utils.cu -o /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.NVCC-depend -ccbin /usr/bin/x86_64-pc-linux-gnu-gcc -m64 -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -Xcompiler ,\"-msse2\",\"-march=amdfam10\",\"-O2\",\"-g\" -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -use_fast_math -ccbin=/usr/bin/x86_64-pc-linux-gnu-gcc -Xcompiler -fPIC -DLINUX -DNVCC -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib/gpu_utils -I/opt/cuda/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/include -I/usr/include -I/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1/src/gmxlib -I/opt/cuda/include
nvcc fatal   : redefinition of argument 'compiler-bindir'
CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:208 (message):
  Error generating
  /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1
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make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float'
make: *** [all] Error 2
 [31;01m*[0m ERROR: sci-chemistry/gromacs-4.6_beta1 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-4.6_beta1'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-4.6_beta1'`.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float'
 [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6-beta1'