ICHEC Software

Information about software packages installed on the ICHEC systems.

GROMACS

Versions Installed

Stokes: 4.0.1 / 4.5.1 / 4.5.5 / 4.6

Stoney: 4.5.5 / 4.6

Description

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but as GROMACS is fast at calculating the nonbonded interactions there is also much research on non-biological systems, e.g. polymers.

On ICHEC's machine, GROMACS is installed with MPI and double precision support enabled, for general usage. In addition, on Stoney, a GPU-enabled version is available as well. However, this one only supports sequential computation (i.e. no MPI or multi-threading) and only for single precision computations. Moreover, only a subset of the features have been ported so far. The GPU version of GROMACS (v4.5.5) relies on the OpenMM library while the latest (v4.6) version has native GPGPU support.

License

GROMACS is available under the GNU General Public License.

Benchmarks

Version 4.6 on Stoney

Taking a 94,124 atom system (membrane protein, explicit solvent) the following image displays the number of nanosecond per day that can be achieved by using CPU-only (blue) compared to CPU-GPGPU (red) of GROMACS v4.6 on Stoney. Using 64 cores (8 nodes) with 16 GPGPUs can result in an additional 17ns/day on top of what the CPU-only version can compute.

Job Submission Example

To run the code in parallel on Stokes or Stoney, please follow this example:

#!/bin/bash
#PBS -N MyJobName
#PBS -j oe
#PBS -r n
#PBS -A MyProjectCode
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:10:00

module load gromacs/4.5.5
# Or v4.6 on Stoney
module load gromacs/4.6

cd $PBS_O_WORKDIR

# pre-process the input for start

# grompp_d -f grompp.mdp -p topol.top -c conf.gro -o water.tpr
grompp_d MyOptions and Files

# start the md

# mpiexec mdrun_d -s water.tpr -o water.trr -c water.out -g water.log
mpiexec mdrun_d MyOptions and files

# v4.6 on Stoney
mpiexec mdrun_mpi_d MyOptions and files

For running the code on Stoney using the GPU version, the above example becomes:

#!/bin/bash
#PBS -N MyJobName
#PBS -j oe
#PBS -r n
#PBS -A MyProjectCode
#PBS -l nodes=1:ppn=8
#PBS -l walltime=00:10:00
#PBS -q GpuQ

module load gromacs/4.5.5
# Or v4.6
module load gromacs/4.6

cd $PBS_O_WORKDIR

# pre-process the input for start

# grompp_d -f grompp.mdp -p topol.top -c conf.gro -o water.tpr
grompp_d MyOptions and Files

# start the md

# mdrun-gpu -s water.tpr -o water.trr -c water.out -g water.log
mdrun-gpu MyOptions and files

# Or v4.6
mpiexec mdrun_mpi MyOptions and files

Additional Notes

Further information can be obtained at www.gromacs.org.

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