Improving molecular dynamics simulation performance on low-cost systems

Teong Han Chew, Kwee Hong Joyce-Tan, Zeti Azura Mohamed Hussein, Pek Iee Elizabeth-Chia, Mohd Shahir Shamsir

Research output: Contribution to journalArticle

Abstract

For simulation-based work, researchers often have limited hardware capacities and budgets, so they create a low-cost parallel computing platform using PCs and commodity hardware, assembled and configured as a Beowulf-class computing cluster. Here, an astute approach (for a molecular dynamics simulation example) greatly improves performance through hardware upgrades and other tricks.

Original languageEnglish
Article number6550014
Pages (from-to)64-70
Number of pages7
JournalComputing in Science and Engineering
Volume15
Issue number3
DOIs
Publication statusPublished - 2013

Fingerprint

Molecular dynamics
Cluster computing
Hardware
Computer simulation
Parallel processing systems
Computer hardware
Costs

Keywords

  • Gromacs
  • low-cost system
  • molecular dynamics
  • NAMD
  • performance comparison
  • performance tuning
  • scientific computing

ASJC Scopus subject areas

  • Computer Science(all)
  • Engineering(all)

Cite this

Improving molecular dynamics simulation performance on low-cost systems. / Chew, Teong Han; Joyce-Tan, Kwee Hong; Mohamed Hussein, Zeti Azura; Elizabeth-Chia, Pek Iee; Shamsir, Mohd Shahir.

In: Computing in Science and Engineering, Vol. 15, No. 3, 6550014, 2013, p. 64-70.

Research output: Contribution to journalArticle

Chew, Teong Han ; Joyce-Tan, Kwee Hong ; Mohamed Hussein, Zeti Azura ; Elizabeth-Chia, Pek Iee ; Shamsir, Mohd Shahir. / Improving molecular dynamics simulation performance on low-cost systems. In: Computing in Science and Engineering. 2013 ; Vol. 15, No. 3. pp. 64-70.
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