Communications overlapping in fast multipole particle dynamics methods
Abstract
In molecular dynamics the fast multipole method (FMM) is an attractive alternative to Ewald summation for calculating electrostatic interactions due to the operation counts. However when applied to small particle systems and taken to many processors it has a high demand for interprocessor communication. In a distributed memory environment this demand severely limits applicability of the FMM to systems with O(10 K atoms). We present an algorithm that allows for fine grained overlap of communication and computation, while not sacrificing synchronization and determinism in the equations of motion. The method avoids contention in the communication subsystem making it feasible to use the FMM for smaller systems on larger numbers of processors. Our algorithm also facilitates application of multiple time stepping techniques within the FMM. We present scaling at a reasonably high level of accuracy compared with optimized Ewald methods.
- Authors:
-
- Department of Computer Science, University of Houston, Houston, TX 77204-5003 (United States)
- Department of Computer Science, University of Houston, Houston, TX 77204-5003 (United States) and Department of Chemistry, University of Houston, 4800 Calhoun, Houston, TX 77204 (United States)
- Publication Date:
- OSTI Identifier:
- 20687220
- Resource Type:
- Journal Article
- Journal Name:
- Journal of Computational Physics
- Additional Journal Information:
- Journal Volume: 203; Journal Issue: 2; Other Information: DOI: 10.1016/j.jcp.2004.09.012; PII: S0021-9991(04)00402-4; Copyright (c) 2004 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9991
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ALGORITHMS; COMMUNICATIONS; EQUATIONS OF MOTION; MOLECULAR DYNAMICS METHOD; SYNCHRONIZATION
Citation Formats
Kurzak, Jakub, and Pettitt, B Montgomery. Communications overlapping in fast multipole particle dynamics methods. United States: N. p., 2005.
Web. doi:10.1016/j.jcp.2004.09.012.
Kurzak, Jakub, & Pettitt, B Montgomery. Communications overlapping in fast multipole particle dynamics methods. United States. https://doi.org/10.1016/j.jcp.2004.09.012
Kurzak, Jakub, and Pettitt, B Montgomery. 2005.
"Communications overlapping in fast multipole particle dynamics methods". United States. https://doi.org/10.1016/j.jcp.2004.09.012.
@article{osti_20687220,
title = {Communications overlapping in fast multipole particle dynamics methods},
author = {Kurzak, Jakub and Pettitt, B Montgomery},
abstractNote = {In molecular dynamics the fast multipole method (FMM) is an attractive alternative to Ewald summation for calculating electrostatic interactions due to the operation counts. However when applied to small particle systems and taken to many processors it has a high demand for interprocessor communication. In a distributed memory environment this demand severely limits applicability of the FMM to systems with O(10 K atoms). We present an algorithm that allows for fine grained overlap of communication and computation, while not sacrificing synchronization and determinism in the equations of motion. The method avoids contention in the communication subsystem making it feasible to use the FMM for smaller systems on larger numbers of processors. Our algorithm also facilitates application of multiple time stepping techniques within the FMM. We present scaling at a reasonably high level of accuracy compared with optimized Ewald methods.},
doi = {10.1016/j.jcp.2004.09.012},
url = {https://www.osti.gov/biblio/20687220},
journal = {Journal of Computational Physics},
issn = {0021-9991},
number = 2,
volume = 203,
place = {United States},
year = {Tue Mar 01 00:00:00 EST 2005},
month = {Tue Mar 01 00:00:00 EST 2005}
}