NAMD: A Portable and Highly Scalable Program for Biomolecular Simulations

Bhatele, Abhinav; Kumar, Sameer; Mei, Chao; Phillips, James C.; Zheng, Gengbin; Kale, Laxmikant V.

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Description

Title

NAMD: A Portable and Highly Scalable Program for Biomolecular Simulations

Author(s)

• Bhatele, Abhinav
• Kumar, Sameer
• Mei, Chao
• Phillips, James C.
• Zheng, Gengbin
• Kale, Laxmikant V.

Issue Date

2009-02

Keyword(s)

• parallel systems
• bioinformatics
• scientific computing

Abstract

NAMD is a portable parallel application for biomolecular simulations. NAMD pioneered the use of hybrid spatial and force decomposition, a technique used by most scalable programs for biomolecular simulations, including Blue Matter and Desmond which were described at Supercomputing 2006. This paper describes parallel techniques and optimizations developed to enhance NAMD's scalability, to exploit recent large parallel machines. NAMD is developed using Charm++ and benefits from its adaptive communication-computation overlap and dynamic load balancing, as demonstrated in this paper. We describe some recent optimizations including: pencil decomposition of the Particle Mesh Ewald method, reduction of memory footprint, and topology sensitive load balancing. Unlike most other MD programs, NAMD not only runs on a wide variety of platforms ranging from commodity clusters to supercomputers, but also scales to thousands of processors. We present results for up to 32,000 processors on machines including IBM's Blue Gene/L, Cray's XT3, and TACC's LoneStar cluster.

Type of Resource

text

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http://hdl.handle.net/2142/11521

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