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ICHEC Software

Information about software packages installed on the ICHEC systems.

DL_POLY

Versions Installed

Fionn: 4.05.1/4.06.1

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.

Benchmarks

4.05.1 on Fionn:

The figure below shows the relative speedup with respect to the number of cores. The benchmark calculation used to obtain these results was TEST40 (available from the DL_POLY ftp site). The figure shows that there is a very good speed up behaviour. Linear speedup is achieved up to 192 cores (8 nodes).

Additional Notes

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

module load molmodel dl_poly/intel/4.05.1

Assuming that this PBS script is saved as dl_poly.pbs, the job can be submitted to the queue by running the following command in the same directory:

qsub dl_poly.pbs

Job Submission Example on Fionn

#!/bin/bash
#PBS -l nodes=2:ppn=24
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the DL_POLY module
module load molmodel dl_poly/intel/4.05.1

cd $PBS_O_WORKDIR

mpiexec DLPOLY.Z
#!/bin/bash
#PBS -l nodes=1:ppn=24
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the DL_POLY module
module load molmodel dl_poly/intel/4.06.1

cd $PBS_O_WORKDIR

mpirun DLPOLY.Z

Job Submission Example on Fionn using GPGPUs

#!/bin/bash
#PBS -l nodes=2:ppn=20
#PBS -l walltime=30:00:00
#PBS -q GpuQ
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the DL_POLY module
module load molmodel dl_poly/intel/4.05.1

cd $PBS_O_WORKDIR

DLPOLY.Z.cu

Further Information

More information can be obtained at http://www.stfc.ac.uk/CSE/randd/ccg/software/DL_POLY/25526.aspx.

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