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Full Record Details
Persistent URL
http://purl.org/net/epubs/work/38112
Record Status
Checked
Record Id
38112
Title
On the performance of molecular dynamics applications on current high-end systems
Contributors
J Hein
,
F Reid
,
L Smith
,
I Bush
,
MF Guest
,
P Sherwood
Abstract
The effective exploitation of current HPC platforms in molecular simulation relies on the ability of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components, including CPUs and memory. In this paper we investigate the efficiency and scaling of a series of popular molecular dynamics codes on the UK's National High Performance Computing Resources, an IBM p690+ cluster and an SGI Altix 3700. Focusing primarily on the AMBER, DL POLY and NAMD simulation codes, we demonstrate the major performance and scalability advantages that arise through a distributed, rather than a replicated data approach.
Organisation
CCLRC
,
CSE
,
CSE-CCG
,
CSE-HEC
Keywords
Chemistry
Funding Information
Related Research Object(s):
Licence Information:
Language
English (EN)
Type
Details
URI(s)
Local file(s)
Year
Journal Article
Philos T Roy Soc A
363 (2005): 1987-1998.
doi:10.1098/rsta.2005.1624
2005
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