ID=29, GROMACS.cuda

• Module/Version: gromacs/2022.3
• Toolchain/Version: gofbc/2020.1.403.114
• CPU instruction set: avx2
• Example job submission script:

  #!/bin/bash
  #SBATCH --mem-per-cpu=2000 --time=10:0:0 -c1 --ntasks=1 --gpus-per-node=v100:1 
  
  export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
  module load ml StdEnv/2020  gcc/9.3.0  cuda/11.4  openmpi/4.0.3 gromacs/2022.3
  gmx mdrun -s topol.tpr -cpi state.cpi

• Benchmark submission script:

    
  #!/bin/bash
  #SBATCH --mem-per-cpu=2000 --time=1:0:0 -c12 --ntasks=1  
  #SBATCH --gpus-per-node=1 --nodes=1 -A def-svassili
  
  td=$SLURM_TMPDIR
  wd=$SLURM_SUBMIT_DIR
  cp topol.tpr $td && cd $td
  module load ml StdEnv/2020  gcc/9.3.0  cuda/11.4  openmpi/4.0.3 gromacs/2022.3
  gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK:-1} \
  -nb gpu -pme gpu -update gpu -bonded cpu -s topol.tpr
  
  # Print CPU info and timing into SLURM log
  grep Brand md.log
  grep -A1 "Number of GPUs detected:" md.log | tail -n1
  grep "The number of OpenMP threads" md.log
  grep Performance: md.log
  cp md.log $wd