DL_POLY

Overview

DL_POLY refers to a suite of general purpose molecular dynamics simulation packages, including

• DL_POLY_4 – version 4 of the STFC codes with a STFC licence and requires MPI2 to allow parallel I/O. Its general parallel approach is domain decomposition. This version is not currently available on the CSF.
• DL_POLY_CLASSIC – (documented on this page) an Open Source branch of DL_POLY_2 with a BSD (ie less restrictive) licence. This is installed on CSF and available to all users. It replicates data to allow parallelism.

Please see Further Info for more details

Running DL_POLY_CLASSIC

The CSF has four versions of DL_POLY_CLASSIC:

To run DL_POLY_CLASSIC

1. load the required modules
2. create your input deck
3. run DLPOLY.X in batch, either in serial or under MPI

Requirements

• the MPI versions were compiled against the Gigabit Ethernet and are not compatible with the Infiniband implementation of MPI
• all versions were compiled with Intel 11.1 compilers

Example

MPI, high optimisation example:

# load the compiler, MPI and DLPOLY modules
module load compilers/intel/fortran/11.1.064
module load mpi/intel-11.1/openmpi/1.4.3 
module load apps/intel-11.1/dl_poly_classic/1.2/parallel-maxOpt
 
# change to user DLPOLY directory, for example (change to suit your own dir names):
cd ~/scratch/sim1

# submit job to 4 cores on Gigabit Ethernet connected nodes
qsub -b y -V -cwd -pe smp.pe 4 mpirun -n 4 DLPOLY.X

An example of the batch submission command as a jobscript:

#!/bin/basg
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 4

mpirun -n $NSLOTS DLPOLY.X

Submit the jobscript thus:

qsub jobscript

where jobscript is the name of your jobscript file.

Running the DL_POLY_CLASSIC Java GUI

Please note that we do not provide support on how to use the GUI. Instructions are given here to launch the GUI but you should consult the DL POLY documentation for help with using the GUI.

The Java GUI allows interactive use of DL POLY. While batch use of DL POLY is preferred (see above) the GUI may be useful when building systems for simulation.

To run the GUI you must create a couple of local directories in your account and copy two system files in to these directories. You then run the GUI from one of these directories. A script is available on the CSF to automate this procedure. Note that it requires that one of the serial DL POLY modules is loaded, as described above. The complete procedure is as follows:

Log in to the CSF with X forwarding enabled

ssh -X username@csf.itservices.manchester.ac.uk

Start a shell on the appropriate compute node. The resource name specified may vary depending on which resources you have access to. Here the short resource is used for a short interactive session

qrsh -l short

In the new shell load the appropriate DL POLY module to set up your environment. You should only use the serial versions interactively (see table above). You should then run the csf_DL_POLY_CLASSIC_gui.sh script to give you a local copy of certain system files before running the gui from the required directory:

module load apps/intel-11.1/dl_poly_classic/1.2/serial-maxOpt   # or serial-lowOpt
csf_DL_POLY_CLASSIC_gui.sh
cd execute
gui

The csf_DL_POLY_CLASSIC_gui.sh script will create an execute/ and java/ directory in your current directory. Ensure you are in the desired directory when you run this command. For example, you may want to first create a directory based on the name of your simulation or molecule and then run the script command from within there. You should then go in to the new execute/ directory. This contains a copy of the DLPOLY.X executable specific to the version specified by the module load command. Running gui from within the execute/ directory will start the Java GUI.

You only need to run the csf_DL_POLY_CLASSIC_gui.sh once if you are using the same version of DLPOLY every time you run it. However, you may want to run it in different directories if running different simulations. Your input decks can be copied to the specific execute/ directory for each simulation.

If you rerun the csf_DL_POLY_CLASSIC_gui.sh script it will copy the DLPOLY.X executable again. This may overwrite a previous version. If you have loaded a different DL POLY module then you will get a different DLPOLY.X file. Please ensure you know which module you have loaded.

Further info

• DL_POLY_CLASSIC
1. CCP Forge web page
2. STFC web page
• DL_POLY
1. STFC web page