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

doi:10.1016/j.jcp.2006.06.014

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

Full Record
Similar

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:

Bowers, Kevin J. ^[1]; Dror, Ron O. ^[1]; Shaw, David E. ^[2]

D. E. Shaw Research, LLC, New York, NY 10036 (United States)
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:: Sat Jan 20 00:00:00 EST 2007

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.

Copy to clipboard


                    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.

Copy to clipboard


                    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.

Copy to clipboard


                    
@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}

}

Copy to clipboard

Journal Article:

DOI: 10.1016/j.jcp.2006.06.014

Other availability

Find in Google Scholar

Search WorldCat to find libraries that may hold this journal

Save / Share:

Export Metadata

Save to My Library

K-means clustering for optimal partitioning and dynamic load balancing of parallel hierarchical N-body simulations

Marzouk, Youssef M. ; Ghoniem, Ahmed F. - Journal of Computational Physics

A number of complex physical problems can be approached through N-body simulation, from fluid flow at high Reynolds number to gravitational astrophysics and molecular dynamics. In all these applications, direct summation is prohibitively expensive for large N and thus hierarchical methods are employed for fast summation. This work introduces new algorithms, based on k-means clustering, for partitioning parallel hierarchical N-body interactions. We demonstrate that the number of particle-cluster interactions and the order at which they are performed are directly affected by partition geometry. Weighted k-means partitions minimize the sum of clusters' second moments and create well-localized domains, and thus reducemore »« less
DOI: 10.1016/j.jcp.2005.01.021
Influence of the parallel nonlinearity on zonal flows and heat transport in global gyrokinetic particle-in-cell simulations

Jolliet, S. ; McMillan, B. F. ; Vernay, T. ; ... - Physics of Plasmas

In this paper, the influence of the parallel nonlinearity on zonal flows and heat transport in global particle-in-cell ion-temperature-gradient simulations is studied. Although this term is in theory orders of magnitude smaller than the others, several authors [L. Villard, P. Angelino, A. Bottino et al., Plasma Phys. Contr. Fusion 46, B51 (2004); L. Villard, S. J. Allfrey, A. Bottino et al., Nucl. Fusion 44, 172 (2004); J. C. Kniep, J. N. G. Leboeuf, and V. C. Decyck, Comput. Phys. Commun. 164, 98 (2004); J. Candy, R. E. Waltz, S. E. Parker et al., Phys. Plasmas 13, 074501 (2006)] found differentmore »« less
DOI: 10.1063/1.3174433
The morphological evolution and internal convection of E{times}B-drifting plasma clouds: Theory, dielectric-in-cell simulations, and N-body dielectric simulations

Borovsky, J.E. ; Hansen, P.J. - Physics of Plasmas

The evolution of {bold E{times}B}-drifting plasma clouds is investigated with the aid of a computational technique denoted here as {open_quotes}dielectric-in-cell.{close_quotes} Many of the familiar phenomena associated with clouds of collisionless plasma are seen and explained and less-well-known phenomena associated with convection patterns, with the stripping of cloud material, and with the evolution of plasma clouds composed of differing ion species are investigated. The effects of spatially uniform diffusion are studied with the dielectric-in-cell technique and with another computational technique denoted as {open_quotes}{ital N}-body dielectric;{close_quotes} the suppression of convection, the suppression of structure growth, the increase in material stripping, and themore »« less
DOI: 10.1063/1.872988
Execution model for limited ambiguity rules and its application to derived data update

Chen, I.M.A. ; Hull, R. ; McLeod, D. - ACM Transactions on Database Systems

A novel execution model for rule application in active databases is developed and applied to the problem of updating derived data in a database represented using a semantic, object-based database model. The execution model is based on the use of `limited ambiguity rules` (LARs), which permit disjunction in rule actions. The execution model essentially performs a breadth-first exploration of alternative extensions of a user-requested update. Given an object-based database scheme, both integrity constraints and specifications of derived classes and attributes are compiled into a family of limited ambiguity rules. A theoretical analysis shows that the approach is sound: the executionmore »« less
DOI: 10.1145/219035.219039
Exact Tensor Hypercontraction: A Universal Technique for the Resolution of Matrix Elements of Local Finite-Range $N$ -Body Potentials in Many-Body Quantum Problems

Parrish, Robert M. ; Hohenstein, Edward G. ; Schunck, Nicolas F. ; ... - Physical Review Letters
DOI: 10.1103/PhysRevLett.111.132505

Full Text Available