On the performance of molecular dynamics applications on current high-end systems.
Philos Trans A Math Phys Eng Sci
; 363(1833): 1987-98, 2005 Aug 15.
Article
en En
| MEDLINE
| ID: mdl-16099762
ABSTRACT
The effective exploitation of current high performance computing (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 HPC 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.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Validación de Programas de Computación
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Programas Informáticos
/
Modelos Moleculares
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Internet
/
Modelos Químicos
Tipo de estudio:
Evaluation_studies
Idioma:
En
Revista:
Philos Trans A Math Phys Eng Sci
Asunto de la revista:
BIOFISICA
/
ENGENHARIA BIOMEDICA
Año:
2005
Tipo del documento:
Article
País de afiliación:
Reino Unido
Pais de publicación:
ENGLAND
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ESCOCIA
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GB
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GREAT BRITAIN
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INGLATERRA
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REINO UNIDO
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SCOTLAND
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UK
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UNITED KINGDOM