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Title: Zonal methods for the parallel execution of range-limited N-body simulations

Abstract

Particle simulations in fields ranging from biochemistry to astrophysics require the evaluation of interactions between all pairs of particles separated by less than some fixed interaction radius. The applicability of such simulations is often limited by the time required for calculation, but the use of massive parallelism to accelerate these computations is typically limited by inter-processor communication requirements. Recently, Snir [M. Snir, A note on N-body computations with cutoffs, Theor. Comput. Syst. 37 (2004) 295-318] and Shaw [D.E. Shaw, A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions, J. Comput. Chem. 26 (2005) 1318-1328] independently introduced two distinct methods that offer asymptotic reductions in the amount of data transferred between processors. In the present paper, we show that these schemes represent special cases of a more general class of methods, and introduce several new algorithms in this class that offer practical advantages over all previously described methods for a wide range of problem parameters. We also show that several of these algorithms approach an approximate lower bound on inter-processor data transfer.

Authors:
 [1];  [1];  [2]
+ Show Author Affiliations
  1. D. E. Shaw Research, LLC, New York, NY 10036 (United States)
  2. D. E. Shaw Research, LLC, New York, NY 10036 (United States) and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032 (United States). E-mail: david@deshaw.com
Publication Date:
OSTI Identifier:
20991555
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Computational Physics; Journal Volume: 221; Journal Issue: 1; Other Information: DOI: 10.1016/j.jcp.2006.06.014; PII: S0021-9991(06)00291-9; Copyright (c) 2006 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ALGORITHMS; ASTROPHYSICS; BIOCHEMISTRY; EVALUATION; MANY-BODY PROBLEM; MATHEMATICAL MODELS; MOLECULAR DYNAMICS METHOD; PARTICLE INTERACTIONS; SIMULATION

Citation Formats

Bowers, Kevin J., Dror, Ron O., and Shaw, David E. Zonal methods for the parallel execution of range-limited N-body simulations. United States: N. p., 2007. Web. doi:10.1016/j.jcp.2006.06.014.
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Bowers, Kevin J., Dror, Ron O., & Shaw, David E. Zonal methods for the parallel execution of range-limited N-body simulations. United States. doi:10.1016/j.jcp.2006.06.014.
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Bowers, Kevin J., Dror, Ron O., and Shaw, David E. Sat . "Zonal methods for the parallel execution of range-limited N-body simulations". United States. doi:10.1016/j.jcp.2006.06.014.
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@article{osti_20991555,
title = {Zonal methods for the parallel execution of range-limited N-body simulations},
author = {Bowers, Kevin J. and Dror, Ron O. and Shaw, David E.},
abstractNote = {Particle simulations in fields ranging from biochemistry to astrophysics require the evaluation of interactions between all pairs of particles separated by less than some fixed interaction radius. The applicability of such simulations is often limited by the time required for calculation, but the use of massive parallelism to accelerate these computations is typically limited by inter-processor communication requirements. Recently, Snir [M. Snir, A note on N-body computations with cutoffs, Theor. Comput. Syst. 37 (2004) 295-318] and Shaw [D.E. Shaw, A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions, J. Comput. Chem. 26 (2005) 1318-1328] independently introduced two distinct methods that offer asymptotic reductions in the amount of data transferred between processors. In the present paper, we show that these schemes represent special cases of a more general class of methods, and introduce several new algorithms in this class that offer practical advantages over all previously described methods for a wide range of problem parameters. We also show that several of these algorithms approach an approximate lower bound on inter-processor data transfer.},
doi = {10.1016/j.jcp.2006.06.014},
journal = {Journal of Computational Physics},
number = 1,
volume = 221,
place = {United States},
year = {Sat Jan 20 00:00:00 EST 2007},
month = {Sat Jan 20 00:00:00 EST 2007}
}
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Journal Article:
DOI:  10.1016/j.jcp.2006.06.014
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