DL-Poly Quick Start

This is a wiki to guide you step by step on how to lauch your first application using HPC Gateway.

For this example, we are using the DL-Poly software that is available already on the system.

DL_POLY Classic is a general purpose molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov. It is based on the package DL_POLY_2, which was originally developed by the former Computational Chemistry Group at Daresbury Laboratory under the auspices of the Engineering and Physical Sciences Research Council (EPSRC), for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5).

DL_POLY Classic can be executed as a serial or parallel application. The code achieves parallelisation using the Replicated Data strategy, which is suitable for homogeneous, distributed-memory, parallel computers. The code is useful for simulations of up to 30,000 atoms with good parallel performance on up to 100 processors, though in some circumstances it can exceed or fail to reach these limits.

Full documentation can be found at: http://www.ccp5.ac.uk/DL_POLY_CLASSIC/

Follow the next steps to run and monitor your first DL-Poly experiment with pre-set datas.

- Login and access the first login desktop

Login using the credentials the HPC Gateway administrator has given you.

First login desktop

- Open DL-Poly wrapper

Double click on DL-PLOY basic icon to open the DL-POLY wrapper.

DL-Poly wrapper

- Select pre-defined bench5 profile

Select pre-defined “bench5” profile on bottom left toolbar. This fills up correct informations to run your first DL-POLY experiment using HPC Gateway.

DL-Poly bench5 profile

- Start bench5 experiment

Click on “Submit” button. A task is submitted to the cluster.

DL-Poly bench5 profile

- Monitor bench5 execution

Open the “Task Monitor” tool from HPC Gateway menu. Get the latest bench5 ID. You can sort columns. A DL-Poly task consist of 3 batch jobs:

  • Prolog job: transfer input files and check application inputs are valid
  • Execute job: this is the real parallel execution of DL-Poly
  • Epilog job: check outputs and transfer back the results

Task monitor tool

- Task details

Click right on the bench5 line and select “Open Task Details” to open the task monitoring window. Open the Run Directory of the execution (Outputs ⇒ RunDir) to access the files that are created during the execution.

Task details menu Task details window

File explorer tool:

Browse the run directory

- Data monitoring

Click right on the bench5 line and select “Open data monitor” to open the main data monitoring window. On the bottom left part,configure 1 or more graphs and follow the evolution of the datas while running.

Data monitor window Data monitor custom graph