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Persistent URL http://purl.org/net/epubs/work/38112
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Record Id 38112
Title On the performance of molecular dynamics applications on current high-end systems
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
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Language English (EN)
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Journal Article Philos T Roy Soc A 363 (2005): 1987-1998. doi:10.1098/rsta.2005.1624 2005