MOLECULAR DYNAMICS PERFORMANCE GUIDE - COMPUTE CANADA

SOFTWARE DETAILS

ID=18, GROMACS.cuda

  • Module/Version: gromacs/2021.2
  • Toolchain/Version: gomklc/2020a
  • CPU instruction set: avx512
  • Example job submission script:
    1. #SBATCH --ntasks=1 --gres=gpu:v100:1 --mem-per-cpu=2000
    2. export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
    3. module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 gromacs/2021.2
    4. gmx_mpi mdrun -s next.tpr -cpi state.cpi
  • Benchmark submission script:
    1. #SBATCH --ntasks=1 --gres=gpu:v100:1 --mem-per-cpu=2000
    2. export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
    3. module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 gromacs/2021.2
    4. gmx_mpi mdrun -s next.tpr -cpi state.cpi