Zonal methods for the parallel execution of range-limited N-body simulations
- 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)
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.
- OSTI ID:
- 20991555
- Journal Information:
- Journal of Computational Physics, Vol. 221, 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); ISSN 0021-9991
- Country of Publication:
- United States
- Language:
- English
Similar Records
An efficient parallel implementation of explicit multirate Runge–Kutta schemes for discontinuous Galerkin computations
Multiscale/Multiphysics Modeling of Biomass Thermochemical Processes