Improving Molecular Dynamics Simulation Performance on Low-Cost Systems

Author

Teong Han Chew ; Joyce-Tan, K.H. ; Hussein, Z.A.M. ; Elizabeth-Chia, P.I. ; Shamsir, M.S.

Author_Institution

Univ. Teknol. Malaysia, Skudai, Malaysia

Volume

15

Issue

3

fYear

2013

fDate

May-June 2013

Firstpage

64

Lastpage

70

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.

Keywords

digital simulation; molecular dynamics method; parallel processing; physics computing; Beowulf-class computing cluster; Gromacs program; Groningen Machine for Chemical Simulations program; MD programs; NAMD program; Not (just) Another Molecular Dynamics program; PC; commodity hardware; low-cost parallel computing platform; low-cost systems; molecular dynamics simulation performance; Costs; Molecular computing; Parallel processing; Performance evaluation; Scientific computing; Simulation; Gromacs; NAMD; low-cost system; molecular dynamics; performance comparison; performance tuning; scientific computing;

fLanguage

English

Journal_Title

Computing in Science & Engineering

Publisher

ieee

ISSN

1521-9615

Type

jour

DOI

10.1109/MCSE.2013.61

Filename

6550014