MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

SOFTWARE DETAILS

ID=21, GROMACS.mpi

  • Module/Version: gromacs/2021.4
  • Toolchain/Version: gofb/2020a
  • CPU instruction set: avx2
  • Example job submission script:

    #!/bin/bash
    #SBATCH --mem-per-cpu=4000 --time=10:0:0 -c1 --ntasks=128 --nodes=2 -A def-svassili

    export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
    module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.4
    srun gmx_mpi mdrun -s topol.tpr -cpi state.cpi

  • Benchmark submission script:
      

    #!/bin/bash
    #SBATCH --mem-per-cpu=4000 --time=10:0:0 -c1 --ntasks=128 --nodes=2 -A def-svassili

    export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
    module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.4
    srun gmx_mpi mdrun -s topol.tpr -cpi state.cpi

    grep Brand md.log
    grep "The number of OpenMP threads" md.log
    grep "MPI pro" md.log
    echo ntasks=$SLURM_TASKS_PER_NODE
    grep Performance: md.log