Using GROMACS

module avail gromacs lists the currently installed versions of Gromacs. All of them are compiled with the intel compiler and allow the usage of GPUs. Our experience showed that Gromacs runs most effective when used with MPI only (no threads) or using GPUs.

You need a script that contains specific information to your job. You find further examples documented.

GROMACS MPI only

A script may look like:

#!/bin/bash					# required
#SBATCH --nodes=2				# using 2 nodes
#SBATCH --ntasks=32				# each with 16 cores
#SBATCH --license=impi				# required 
#SBATCH --constraint=XEON_E5_2640v3&HT:off	# processor type without Hyperthreading

module load intel/2015
module load gromacs/5.0				# or another version

if [ "$1" == "" ]; then
   echo "input file name is missing"
   exit
fi
echo "Gromacs with input $1"
mpirun mdrun_icc_impi1 -deffnm $1

This script may be called gromacs_mpi.sh and is submit via

sbatch gromacs_mpi.sh input 

GROMACS with GPUs

A script may look like:

#!/bin/bash				# required
#SBATCH --nodes=1			# using 1 nodes
#SBATCH --ntasks=16			# with all its 16 cores
#SBATCH --gres=gpu:4,gpu_ccc:35		# 4 gpus, at least compute capability 3.5

module load intel/2015
module load gromacs/5.0				# or another version

if [ "$1" == "" ]; then
   echo "input file name is missing"
   exit
fi
echo "Gromacs with input $1"
mdrun_cuda -deffnm $1