MOLECULAR DYNAMICS PERFORMANCE GUIDE - COMPUTE CANADA

SOFTWARE DETAILS

ID=21, GROMACS.mpi

  • Module/Version: gromacs/2021.4
  • Toolchain/Version: gofb/2020a
  • CPU instruction set: avx2
  • Example job submission script:
    1. #!/bin/bash
    2. #SBATCH --mem-per-cpu=4000 --time=10:0:0 -c1 --ntasks=128 --nodes=2 -A def-svassili
    3. export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
    4. module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.4
    5. srun gmx_mpi mdrun -s topol.tpr -cpi state.cpi
  • Benchmark submission script:
    1. #!/bin/bash
    2. #SBATCH --mem-per-cpu=4000 --time=10:0:0 -c1 --ntasks=128 --nodes=2 -A def-svassili
    3. export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
    4. module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.4
    5. srun gmx_mpi mdrun -s topol.tpr -cpi state.cpi
    6. grep Brand md.log
    7. grep "The number of OpenMP threads" md.log
    8. grep "MPI pro" md.log
    9. echo ntasks=$SLURM_TASKS_PER_NODE
    10. grep Performance: md.log