Gromacs

Introduction

Gromacs is freely available and open source software.

Setting the module environment

A number of versions of Gromacs are available on the facility.

To load gromacs into your environment when you log in, use (for example):

$ module add gromacs/4.5.3

This will now provide you with access to the gromacs executeables from the command line.

Alternatively you can load the default version of gromacs installed on ARC with the command:

$ module add gromacs

Will load the executables for the default 4.6.3 version.

Executable naming conventions

The main executables available are :

Executable

Description

mdrun

single precision serial executable

mdrun_d

double precision serial executable

mpirun mdrun_mpi

single precision parallel MPI executable

mpirun mdrun_mpi_d

double precision parallel MPI exectable

However, the naming convention for Gromacs versions below 4.6.3 are a little different:

Executable

Description

mdrun.MPI

single precision, parallel MPI executable

mdrun_d.MPI

double precision, parallel MPI executable

There are also single/double precision versions of the tools that come with the application, with the same naming scheme as above. For more information look at the Gromacs homepage and at the Gromacs documentation.

Batch execution

Serial execution

An example job submission script (example_serial.sh) that runs a gromacs executeable is shown below:

#!/bin/bash
#$ -cwd -V 
# request 10 hours of runtime
#$ -l h_rt=10:00:00
mdrun_d  <args>

This requests 10 hours of runtime, to run in the current directory -cwd and using the current environment -V, using the double precision version of mdrun, and where <args> represents the arguments to mdrun. More memory per core can be requested, 2Gb for instance, by adding the line #$ -l h_vmem=2G to the script. You can find more submission options on the batch job page.

The script can be submitted with:

$ qsub example_serial.sh

Parallel execution

An example submission script (example_parallel.sh) looking to use the parallel executeable is shown below:

#!/bin/bash
#$ -cwd -V
# request 10 hours of runtime
#$ -l h_rt=10:00:00
# request 4 cores
#$ -pe ib 4
mpirun mdrun_mpi_d <args>

This requests 10 hours of runtime, to run in the current directory -cwd, using the current environment -V, running on 4 cores -pe ib 4, using the double precision parallel version of mdrun, and where <args> represents the arguments to mdrun .

More memory per core can be requested, 2Gb for instance, by adding the line #$ -l h_vmem=2G to the script. You can find more submission options on the batch job page.

The script can be submitted with:

$ qsub example_parallel.sh