Scalability of DL_POLY on High Performance Computing Platform

Authors

  • Mabule Samuel Mabakane Council for Scientific and Industrial Research (CSIR), Centre for High Performance Computing and University of Cape Town (UCT)
  • Daniel Mojalefa Moeketsi Council for Scientific and Industrial Research (CSIR), Centre for High Performance Computing (CHPC)
  • Anton Lopis Council for Scientific and Industrial Research (CSIR), Centre for High Performance Computing (CHPC)

DOI:

https://doi.org/10.18489/sacj.v29i3.405

Keywords:

E1350 IBM Linux cluster, Sun system, Lengau supercomputer, Ethernet network, Infiniband network, DL_POLY, weak scalability, strong scalability

Abstract

This paper presents a case study on the scalability of several versions of the molecular dynamics code (DL_POLY) performed on South Africa‘s Centre for High Performance Computing e1350 IBM Linux cluster, Sun system and Lengau supercomputers. Within this study different problem sizes were designed and the same chosen systems were employed in order to test the performance of DL_POLY using weak and strong scalability. It was found that the speed-up results for the small systems were better than large systems on both Ethernet and Infiniband network. However, simulations of large systems in DL_POLY performed well using Infiniband network on Lengau cluster as compared to e1350 and Sun supercomputer.

Author Biographies

Mabule Samuel Mabakane, Council for Scientific and Industrial Research (CSIR), Centre for High Performance Computing and University of Cape Town (UCT)

Senior. Systems administrator at Centre for High Performance Computing under the auspices of the Council for Scientific and Industrial Research and PhD student: Computer Science at the University of Cape Town, Faculty of Science, Department of Computer Science.

Daniel Mojalefa Moeketsi, Council for Scientific and Industrial Research (CSIR), Centre for High Performance Computing (CHPC)

Senior Research Scientist at CSIR, CHPC

Anton Lopis, Council for Scientific and Industrial Research (CSIR), Centre for High Performance Computing (CHPC)

Senior Research Scientist at CSIR, CHPC

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Published

2017-12-08

Issue

Vol. 29 No. 3 (2017)

Section

Research Papers (general)

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