DL_POLY

Introduction

DL_POLY is a general purpose molecular dynamics simulation tool developed and provisioned for UK academia. You can read more about it on the DL_POLY web page.

Licensing

To access this software you need to agree to the license terms, please submit a request to the Research Computing team via our contact form confirming you accept the license terms and wish to be added to the DL_POLY user group.

The licence terms are available on the DLpoly license page.

Loading the module

DL_POLY versions 4.08 and 4.09 are currently available on ARC3 and 4.09 and 4.10 on ARC4. You can add the DL_POLY module by using a command like this:

$ module add dl_poly/4.09

This adds the DL_POLY 4.09 executable files to your environment and must be included in your job submission script to ensure your jobs can also access DL_POLY.

Usage

DL_POLY 4.09/4.10

DL_POLY 4.09/4.10 is built with to both run in serial and in parallel depending on the resources available using the single executable DLPOLY.Z.

Parallel execution

An example job submission script that calls DLpoly is shown below:

#$ -cwd -V
#$ -l h_rt=48:00:00
#$ -pe ib 16
module add dl_poly/4.10
mpirun -np $NSLOTS DLPOLY.Z

This requests 48 hours of runtime on 16 processes spread over Infiniband. Saved as dlpoly.sh this can be submitted to the queue with the command:

$ qsub dlpoly.sh

Serial execution

DL_POLY can be run in serial using the same executable without prepending the call with mpirun.

#$ -cwd -V
#$ -l h_rt=48:00:00
module add dl_poly/4.10
DLPOLY.Z

To submit the above script do:

$ qsub dlpoly_serial.sh

DL_POLY 4.08

Version 4.08 is built on ARC3 and has a slightly different executable that can be used as follows:

Job submission example

An example job submission script that calls to the DL_POLY.Z.parallel executable and requests multiple cores over Infiniband.

#$ -cwd -V
#$ -l h_rt=48:00:00
#$ -pe ib 16
module add dl_poly/4.08
mpirun DLPOLY.Z.parallel

The same executable can also be used to run a job in serial.