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GROMACS

AiMOS Install

Load Needed Modules

module load gcc/8.4.0/1 module load cmake module load spectrum-mpi module load cuda/10.2

Build FFTW3 (prerequisite for GROMACS)

  1. Download FFTW3 source - latest version.
  2. Upload to CCI home directory
  3. Untar file
  4. Run configure command in source directory as follows:

    ./configure --prefix=/gpfs/u/home/[Project ID]/[User ID]/scratch-shared/install --enable-shared --enable-float
    
  5. Issue "make" command

    make -j 8
    
  6. Issue "install" command

    make install
    

Build GROMACS

  1. Download 2020.1 version of GROMACS
  2. Upload to CCI home directory
  3. Untar file
  4. Edit gromacs-2020.1/cmake/gmxManageNvccConfig.cmake and remove CUDA_NVCC_FLAGS and replace with -Xcompiler -mno-float128
  5. Issue "cmake" command (in a one line command that wraps around) in build directory as follows:

    cmake ../gromacs-2020.1/ -DGMX_GPU=on -DGMX_MPI=on -DGMX_CUDA_TARGET_SM=70 -DGMX_OPENMP_MAX_THREADS=128 -DCMAKE_C_COMPILER=gcc  -DCMAKE_CXX_COMPILER=g++ -DGMX_SIMD=IBM_VSX -DCAMKE_CXX_FLAGS="-O3 -mcpu=power9 -mvsx" -DCMAKE_C_FLAGS="-O3 -mcpu=power9 -mvsx" -DFFTWF_LIBRARY=/gpfs/u/home/[Project ID]/[User ID]/scratch-shared/install/lib/libfftw3f.so -DFFTWF_INCLUDE_DIR=/gpfs/u/home/[Project ID]/[User ID]/scratch-shared/install/include/
    
  6. Issue "make" command:

    make -j 8
    
  7. GROMACS binary is in the [path-to-gromacs-build]/bin/ directory.


Last update: May 14, 2020