MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

SOFTWARE DETAILS

ID=35, OPENMM.cuda

  • Module/Version: openmm/8.0.0
  • Toolchain/Version: gofbc/2020.1.403.114
  • CPU instruction set: avx512
  • Example job submission script:

    #!/bin/bash
    #SBATCH -c1 --gpus-per-node=v100:1
    #SBATCH --mem-per-cpu=4000 --time=1:0:0

    module purge
    ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 ambertools/23
    ml openmm/8.0.0 netcdf/4.7.4 hdf5/1.10.6 mpi4py/3.0.3

    virtualenv \${SLURM_TMPDIR}/env
    source \${SLURM_TMPDIR}/env/bin/activate
    pip install --no-index netCDF4

    python openmm_input.py

  • Benchmark submission script:
      

    #!/bin/bash
    #SBATCH -c1 --gpus-per-node=v100:1
    #SBATCH --mem-per-cpu=4000 --time=1:0:0

    module purge
    ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 ambertools/23
    ml openmm/8.0.0 netcdf/4.7.4 hdf5/1.10.6 mpi4py/3.0.3

    virtualenv ${SLURM_TMPDIR}/env
    source ${SLURM_TMPDIR}/env/bin/activate
    pip install --no-index netCDF4

    python openmm_input.py