The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.
DL_POLY_4 is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov, W. Smith, A.M. Elena and others.
After connecting to Bessemer (see Establishing a SSH connection), start an interactive session with the
srun --pty bash -i command.
The latest version of DL_POLY_4 (currently version 5.0.0) is made available with the command:
$ module load DL_POLY_4_PLUMED_INTEG/5.0.0-intel-2020b
After this the DL_POLY_4 command can be run from the terminal prompt
Users are encouraged to write their own batch submission scripts. The following is an example batch
my_job.sh, to run
DLPOLY.Z and which is submitted to the queue by typing
#!/bin/bash #SBATCH --job-name=DL_POLY_4_test #SBATCH --nodes=1 #SBATCH --ntasks-per-node=8 #SBATCH --mem=2000 #SBATCH --time=00:30:00 #SBATCH --firstname.lastname@example.org #SBATCH --mail-type=ALL module load DL_POLY_4_PLUMED_INTEG/5.0.0-intel-2020b # Get Example 2 from the DL_POLY website. # ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/Tutorial_Notes.pdf wget ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/Exercise2.tar.gz tar -xvf Exercise2.tar.gz cd Exercise2 mpirun -np $SLURM_NTASKS DLPOLY.Z
DL_POLY_4 version 5.0.0 was installed using Easybuild 4.4.0 and was optionally interfaced
with the PLUMED 2.6.2 library. build details can be found in
Installation was tested as with the above batch script with example 2 directly taken from ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/) with the following decomposeParDict: https://openfoamwiki.net/index.php/DecomposePar