benchmark GROMACS with NVIDIA GPU Cloud (NGC) Docker container

run_adh_cubic.sh

#!/bin/bash

wget https://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz
tar xvzf ADH_bench_systems.tar.gz
docker run -ti --runtime nvidia -v $(pwd)/ADH/adh_cubic:/benchmark --workdir /benchmark nvcr.io/hpc/gromacs:2020.2 sh -c "gmx grompp -f pme_verlet.mdp"
time docker run -ti --runtime nvidia -v $(pwd)/ADH/adh_cubic:/benchmark --workdir /benchmark nvcr.io/hpc/gromacs:2020.2 sh -c "gmx mdrun -v -nsteps 100000 -resetstep 90000 -noconfout -ntmpi 4 -ntomp 10 -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400 -s topol.tpr"