DL_POLY on WestGrid Systems
Introduction
DL_POLY is a suite of programs developed at Daresbury Laboratory for molecular dynamics simulations of a variety of systems, including "macromolecules, polymers, ionic systems and solutions".
The software is licensed for academic, non-commercial use to individual researchers. In accordance with section 2.3 of the license agreement, WestGrid makes the software available only to researchers who have registered at http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml , agreeing to the license terms given there. If you have completed that registration and would like to use the DL_POLY software on WestGrid systems, please send a signed email to support@westgrid.ca with the subject line: "DL_POLY access request (user name)", substituting your WestGrid user name. In response, a request will be sent to the WestGrid system administrators to add your user name to the UNIX group wg-dlpol. Only members of that group have access to the directory in which the DL_POLY software is located. It may take a day or two for the request to be processed.
Users are expected to be generally familiar with DL_POLY capabilities and input file formats. In particular, you must decide whether DL_POLY 2 or DL_POLY 3 is most appropriate for your work. DL_POLY 3 can handle much larger systems than DL_POLY 2 due to a different parallelization strategy. In some cases, benchmarking with both versions may be needed to make the best choice.
Running DL_POLY on Matrix
The DL_POLY software has been installed in /usr/apps/dl_poly in version-specific subdirectories.
Like other jobs on WestGrid systems, DL_POLY jobs are run by submitting an appropriate script for batch scheduling using the qsub command.
Details of scheduling and job management are explained on the Running Jobs page, but, a simple example is given below.
The following command submits a DL_POLY 3 job script, dlpoly3.pbs, to run on eight processors:
qsub -l nodes=4:ppn=2 dlpoly3.pbs
where dlpoly3.pbs is:
#!/bin/bash
#PBS -S /bin/bash
# Script for running a single DL_POLY 3 test
# from the distributed DL_POLY 3 test suite.
# The TESTNUM variable below is used to select
# the test to use from the DL_POLY data directory.
# 2007-10-16 DSP
DLPOLY3=/usr/apps/dl_poly/dl_poly_3.08
cd $PBS_O_WORKDIR
echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
# Set up a directory for the run
ROOT="dlpoly3_test"
TESTNUM=1
mkdir ${ROOT}${TESTNUM}
cd ${ROOT}${TESTNUM}
ln -fs ${DLPOLY3}/execute/DLPOLY.Y DLPOLY.Y
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/CONTROL CONTROL
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/FIELD FIELD
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/CONFIG CONFIG
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/TABLE TABLE
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/TABEAM TABEAM
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/REFERENCE REFERENCE
echo "Current directory: `pwd`"
echo "Starting run at: `date`"
MY_PROG="DLPOLY.Y"
/usr/apps/bin/PBS_mpirun $MY_PROG
echo "Job finished with exit code $? at: `date`"
#PBS -S /bin/bash
# Script for running a single DL_POLY 3 test
# from the distributed DL_POLY 3 test suite.
# The TESTNUM variable below is used to select
# the test to use from the DL_POLY data directory.
# 2007-10-16 DSP
DLPOLY3=/usr/apps/dl_poly/dl_poly_3.08
cd $PBS_O_WORKDIR
echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
# Set up a directory for the run
ROOT="dlpoly3_test"
TESTNUM=1
mkdir ${ROOT}${TESTNUM}
cd ${ROOT}${TESTNUM}
ln -fs ${DLPOLY3}/execute/DLPOLY.Y DLPOLY.Y
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/CONTROL CONTROL
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/FIELD FIELD
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/CONFIG CONFIG
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/TABLE TABLE
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/TABEAM TABEAM
ln -fs ${DLPOLY3}/data/TEST${TESTNUM}/REFERENCE REFERENCE
echo "Current directory: `pwd`"
echo "Starting run at: `date`"
MY_PROG="DLPOLY.Y"
/usr/apps/bin/PBS_mpirun $MY_PROG
echo "Job finished with exit code $? at: `date`"
The dlpoly3.pbs script is available on Matrix as /usr/apps/examples/dlpoly/dlpoly3.pbs . The DL_POLY software is normally run so that input and output files are referenced relative to the directory containing the executable, DLPOLY.Y . However, by linking to the executable, as shown in the example, on the line:
ln -fs ${DLPOLY3}/execute/DLPOLY.Y DLPOLY.Y
you do not have to make your own copy of the software in every job directory.
Running DL_POLY on Cortex
DL_POLY 2 and DL_POLY 3 are available on the WestGrid Cortex system under /ibm_global/dl_poly. Sample job submission scripts are not currently available. Please write to support@westgrid.ca if you need assistance running the software on Cortex.
Updated 2007-10-16.
