MOLECULAR DYNAMICS PERFORMANCE GUIDE - COMPUTE CANADA

SOFTWARE DETAILS

ID=19, GROMACS.mpi

  • Module/Version: gromacs/2021.2
  • Toolchain/Version: gomkl/2020.a
  • CPU instruction set: avx512
  • Example job submission script:
    1. #!/bin/bash
    2. #SBATCH --mem-per-cpu=4000 --time=10:0:0 -c1 --ntasks=80 --nodes=2
    3. export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
    4. module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.2
    5. srun gmx_mpi mdrun -s topol.tpr -cpi state.cpi
  • Benchmark submission script:
    1. #!/bin/bash
    2. #SBATCH --mem-per-cpu=4000 --time=10:0:0 -c1 --ntasks=80 --nodes=2
    3. export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
    4. module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.2
    5. srun gmx_mpi mdrun -s topol.tpr -cpi state.cpi