Article

NAMD: biomolecular simulation on thousands of processors

Authors:

James C. Phillips,

Gengbin Zheng,

Sameer Kumar,

Laxmikant V. KaléAuthors Info & Claims

SC '02: Proceedings of the 2002 ACM/IEEE conference on Supercomputing

Pages 1 - 18

Published: 16 November 2002 Publication History

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Abstract

NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoffelectrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.

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Krašovec BFilipă?Iă? A(2019)Enhancing the Grid with Cloud ComputingJournal of Grid Computing10.1007/s10723-018-09472-w17:1(119-135)Online publication date: 1-Mar-2019
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Lindow NBaum DHege HByška JKrone MSommer B(2018)Atomic accessibility radii for molecular dynamics analysisProceedings of the Workshop on Molecular Graphics and Visual Analysis of Molecular Data10.5555/3293503.3293506(9-17)Online publication date: 4-Jun-2018
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NAMD: biomolecular simulation on thousands of processors

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Information & Contributors

Information

Published In

SC '02: Proceedings of the 2002 ACM/IEEE conference on Supercomputing

November 2002

952 pages

ISBN:076951524X

Conference Chair:
Roscoe Giles
Boston University
,
Program Chair:
Daniel Reed
NCSA
,
Publications Chair:
Kathryn Kelley
Ohio Supercomputer Center

Publisher

IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 16 November 2002

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Article

Conference

SC '02

Sponsor:

SIGARCH
IEEE-CS

SC '02: International Conference for High Performance Computing, Networking, Storage and Analysis

16 11 2002

Maryland, Baltimore

Acceptance Rates

SC '02 Paper Acceptance Rate 67 of 230 submissions, 29%;

Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

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Krašovec BFilipă?Iă? A(2019)Enhancing the Grid with Cloud ComputingJournal of Grid Computing10.1007/s10723-018-09472-w17:1(119-135)Online publication date: 1-Mar-2019
https://dl.acm.org/doi/10.1007/s10723-018-09472-w
Lindow NBaum DHege HByška JKrone MSommer B(2018)Atomic accessibility radii for molecular dynamics analysisProceedings of the Workshop on Molecular Graphics and Visual Analysis of Molecular Data10.5555/3293503.3293506(9-17)Online publication date: 4-Jun-2018
https://dl.acm.org/doi/10.5555/3293503.3293506
Duan XGao PZhang TZhang MLiu WZhang WXue WFu HGan LChen DMeng XYang G(2018)Redesigning LAMMPS for peta-scale and hundred-billion-atom simulation on Sunway TaihuLightProceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis10.5555/3291656.3291672(1-12)Online publication date: 11-Nov-2018
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Tang XZhai JQian XHe BXue WChen W(2018)vSensorACM SIGPLAN Notices10.1145/3200691.317849753:1(124-136)Online publication date: 10-Feb-2018
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Duan XGao PZhang TZhang MLiu WZhang WXue WFu HGan LChen DMeng XYang G(2018)Redesigning LAMMPS for peta-scale and hundred-billion-atom simulation on Sunway TaihuLightProceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis10.1109/SC.2018.00015(1-12)Online publication date: 11-Nov-2018
https://dl.acm.org/doi/10.1109/SC.2018.00015
Malhotra DBiros G(2016)Algorithm 967ACM Transactions on Mathematical Software10.1145/289834943:2(1-27)Online publication date: 16-Aug-2016
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Jain NBhatele ANi XWright NKale LDamkroger TDongarra J(2014)Maximizing throughput on a dragonfly networkProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1109/SC.2014.33(336-347)Online publication date: 16-Nov-2014
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Kunaseth MKalia RNakano ANomura KVashishta PGropp WMatsuoka S(2013)A scalable parallel algorithm for dynamic range-limited n-tuple computation in many-body molecular dynamics simulationProceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis10.1145/2503210.2503235(1-12)Online publication date: 17-Nov-2013
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