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NAMD: A Portable and Highly Scalable Program for Biomolecular Simulations

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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.
Subject(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.
Issue Date: 2009-02
Genre: Technical Report
Type: Text
URI: http://hdl.handle.net/2142/11521
Other Identifier(s): UIUCDCS-R-2009-3034
Rights Information: You are granted permission for the non-commercial reproduction, distribution, display, and performance of this technical report in any format, BUT this permission is only for a period of 45 (forty-five) days from the most recent time that you verified that this technical report is still available from the University of Illinois at Urbana-Champaign Computer Science Department under terms that include this permission. All other rights are reserved by the author(s).
Date Available in IDEALS: 2009-04-23
 

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