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DL_POLY

DL_POLY#

Versions Installed

Kay: 4.09

LXP:

Description#

DL_POLY is a package of subroutines, programs and data files, designed to facilitate molecular dynamics simulations of macromolecules, polymers, ionic systems and solutions on a distributed memory parallel computer. DL_POLY was developed at the STFC Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov. Three versions of DL_POLY are currently available:

DL_POLY_2 is the original version which has been parallelised using the Replicated Data strategy and is useful for simulations of up to 30,000 atoms on 100 processors.

DL_POLY_3 is a version which uses Domain Decomposition to achieve parallelism and is suitable for simulations of order 1 million atoms on 8-1024 processors.

DL_POLY_4’s general design provides scalable performance from a single processor workstation to a high performance parallel computer. DL_POLY_4 offers fully parallel I/O as well as a netCDF alternative (HDF5 library dependence) to the default ASCII trajectory file. It is also available as a CUDA+OpenMP port, developed in collaboration with ICHEC, to harness the power offered by NVIDIA® GPUs. A full description of the available DL_POLY_4 functionality may be obtained from the DL_POLY_4 User Manual (PDF).

License#

Currently, only one version of the DL_POLY software is available under an STFC license, DL_POLY_4, and with support provisioned to the UK’s academia only. The former DL_POLY_2 version (authored by W. Smith, T.R. Forester and I.T. Todorov) is now transformed into DL_POLY_CLASSIC and available as open source under the BSD license.

Users should express their interest to the Helpdesk to gain access to the executables.

Additional Notes#

To use a version of DL_POLY on Fionn load the relevant environment module:

module load dlpoly/4.09

Assuming that the following SLURM script is saved as dlpoly.sub, the job can be submitted to the queue by running the following command in the same directory:

sbatch dlpoly.sub

Job Submission Example on Fionn#

#!/bin/sh
# All the information about queues can be obtained using 'sinfo'

# PARTITION AVAIL  TIMELIMIT  

# DevQ         up    1:00:00   
# ProdQ*       up 3-00:00:00    
# LongQ        up 6-00:00:00    
# ShmemQ       up 3-00:00:00    
# PhiQ         up 1-00:00:00   
# GpuQ         up 2-00:00:00    

# Slurm flags

#SBATCH -p ProdQ
#SBATCH -N 1
#SBATCH -t 02:00:00
#SBATCH --job-name=dlpolyJob

# Charge job to myproject 
#SBATCH -A MyProject

# Write stdout+stderr to file
#SBATCH -o output.txt

# Mail me on job start & end
#SBATCH --mail-user=myEmail@domain.ie
#SBATCH --mail-type=BEGIN,END

cd $SLURM_SUBMIT_DIR

module load dlpoly/4.09
mpirun -np 4 DLPOLY.Z > output

Further information#

More information can be obtained here.

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