DL_POLY Environment Modules - Version 4.08

This is a guide for DL_POLY on Hodor using environment Modules

STEP ONE - Load Modules.

In order to use DL_POLY on the Hodor cluster you will need to load the module.

Loading the DL poly module will also load any dependencies.

Ex.

module load dl_poly/4.09-mpi

This will load the mpich implementaion of dl_poly and the mpich gcc modules that are dependencies.

If you receieve the following error

ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'dl_poly/4.09-mpi'

The other implementaions we currently have are dl_poly/4.08-mpi, dl_poly/4.08-intelmpi and dl_poly/4.08-serial.

STEP TWO - Submitting to the Queue.

In order to have your trial of the program run on the cluster you have to create a script that will get put in the queue.

Before you submit your run to the queue, make sure you have all the required files and the submission script in one directory. Following is an example script that can be used to put your task in the queue.

dl_poly_submit.sh:

#!/bin/bash
#####Number of nodes
#SBATCH -N1
#####Number of tasks per node
#SBATCH --ntasks-per-node=8
#SBATCH --mem-per-cpu=2G
#SBATCH --job-name=DL_POLY
#SBATCH --workdir=./
#SBATCH -o slurm_run_%j_output.txt
#SBATCH -e slurm_run_%j_error.txt

#Changes working directory to the location where you submitted this script from
printf 'Changing to the working directory: %s\n\n' "$SLURM_SUBMIT_DIR"
cd $SLURM_SUBMIT_DIR

#Load Necessary Modules to Run the Program
printf 'Loading modules\n'
module load dl_poly/4.08-mpi

#Determine the job host names and write a hosts file
srun -n $SLURM_NTASKS hostname | sort -u > ${SLURM_JOB_ID}.hosts

#Run DLPOLY.Z using MPIRUN
printf 'running DLPOLY.Z\n'
mpirun -np $SLURM_NTASKS -machinefile ${SLURM_JOB_ID}.hosts DLPOLY.Z

Now with the required files (CONTROL, CONFIG, FIELD), the submission file dl_poly_submit.sh, and any other files your run might need (eg. REVIVE or REVCON) you are ready to submit the script to slurm. This can be done using the following command:

sbatch dl_poly_submit.sh

NOTE: For more detailed dl_poly usage information be sure to read the user manual (ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf)

For more information about submitting jobs, Slurm, and its commands view our tutorial HERE.