Communications overlapping in fast multipole particle dynamics methods

Jakub Kurzak, B. Montgomery Pettitt

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)731-743
Number of pages13
JournalJournal of Computational Physics
Volume203
Issue number2
DOIs
StatePublished - Mar 1 2005
Externally publishedYes

ASJC Scopus subject areas

  • Numerical Analysis
  • Modeling and Simulation
  • Physics and Astronomy (miscellaneous)
  • Physics and Astronomy(all)
  • Computer Science Applications
  • Computational Mathematics
  • Applied Mathematics

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