[gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ??

[Mark Abraham]

On Thu, Nov 20, 2014 at 12:08 AM, Soren Wacker <swacker at ucalgary.ca> wrote:

> Hi,
>
> another question:
> Is it possible to install gromacs  5.0.2 with CUDA and MPI?
>

Yes, but you should use a compiler version that is supported by your CUDA
version, and not try to install release candidate versions Gromacs. ;-)

Mark


> Since, when I try to generate mdrun_mpi everything seems to work fine until
> >make install
>
> then I get some cryptic error messages.
>
> Some details first:
> ------
> Intel(R) Xeon(R) CPU           X5550  @ 2.67GHz
> # Set up environment to work with the Intel 12.1.4 compilers
>
> openmpi/1.6.5
> intel/2011-sp1.10.319 (intel 12.1.4 or 12.1.0 compiler)
> cuda/6.0            (also tried cuda 5.5)
>
> >mpicc -v
> icc version 12.1.4 (gcc version 4.4.7 compatibility)
>
> input commands:
> CC=mpicc \
> CXX=mpiCC \      (also tried mpicxx)
> cmake ${SOURCE_DIR} \
>  -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} \
>  -DFFTWF_INCLUDE_DIR=$FFTWSINGLE/include \
>  -DFFTWF_LIBRARY=$FFTWSINGLE/lib/libfftw3f.a \
>  -DCMAKE_PREFIX_PATH="/global/software/boost/gcc" \
>  -DCMAKE_PREFIX_PATH="$FFTWSINGLE" \
>  -DGMX_BUILD_MDRUN_ONLY=ON \
>  -DGMX_MPI=on \
>  -DGMX_SIMD="SSE4.1"
> --------
>
>
>
>
> Here the output:
>
> -- Configuring done
> -- Generating done
> -- Build files have been written to:
> /home/@USER/Install_Software/gromacs/builds/gromacs_50rc1_intel1214_sharedfftw3_openmp_sse41_mpi_single
> Scanning dependencies of target git-version-info
> Scanning dependencies of target mdrun_objlib
> [  0%] Generating git version information
> [  1%] [  1%] [  1%] Building CXX object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o
> Building C object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
> Building CXX object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.cpp.o
> warning #13000: could not open message catalog file:  diagsc.cat
> warning #13000: could not open message catalog file:  diagsc.cat
> warning #13000: could not open message catalog file:  diagsc.cat
> [  1%] Built target git-version-info
> [  1%] Building CXX object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.cpp.o
> warning #13000: could not open message catalog file:  diagsc.cat
> [  1%] Building CXX object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
> [  1%] [  1%] Building NVCC (Device) object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o
> Generating baseversion-gen.c
> [  1%] warning #13000: could not open message catalog file:  diagsc.cat
> Building NVCC (Device) object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o
> icc: command line warning #10006: ignoring unknown option '-dumpspecs'
> icc: command line error: no files specified; for help type "icc -help"
> CMake Error at libgromacs_generated_cudautils.cu.o.cmake:206 (message):
>   Error generating
>
> /home/@USER/Install_Software/gromacs/builds/gromacs_50rc1_intel1214_sharedfftw3_openmp_sse41_mpi_single/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o
>
>
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> icc: command line warning #10006: ignoring unknown option '-dumpspecs'
> icc: command line error: no files specified; for help type "icc -help"
> CMake Error at libgromacs_generated_copyrite_gpu.cu.o.cmake:206 (message):
>   Error generating
>
> /home/@USER/Install_Software/gromacs/builds/gromacs_50rc1_intel1214_sharedfftw3_openmp_sse41_mpi_single/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o
>
>
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o]
> Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs....
> [  1%] Built target mdrun_objlib
> make: *** [all] Error 2
> [  0%] Generating git version information
> [  0%] Built target git-version-info
> [  0%] Building NVCC (Device) object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o
> icc: command line warning #10006: ignoring unknown option '-dumpspecs'
> icc: command line error: no files specified; for help type "icc -help"
> CMake Error at libgromacs_generated_cudautils.cu.o.cmake:206 (message):
>   Error generating
>
> /home/@USER/Install_Software/gromacs/builds/gromacs_50rc1_intel1214_sharedfftw3_openmp_sse41_mpi_single/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o
>
>
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o]
> Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
> Finished installing MPI single-precision version of mdrun at Wed Nov 19
> 15:34:18 MST 2014
>
>
> --
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