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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/11.2

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
  1. Issue "make" command
make -j 8
  1. 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 to remove CUDA_NVCC_FLAGS and replace with -Xcompiler -mno-float128 A patch file is available at /gpfs/u/software/dcs/patches/gromacs-2020.1-no-float128.patch to make this change automatically

  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 -DCMAKE_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/
  1. Issue "make" command:
make -j 8
  1. GROMACS binary is in the [path-to-gromacs-build]/bin/ directory.