Communications overlapping in fast multipole particle dynamics methods

Jakub Kurzak, Bernard Pettitt

Research output: Contribution to journalArticle

12 Citations (Scopus)

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

Fingerprint

multipoles
communication
Communication
central processing units
interprocessor communication
distributed memory
Coulomb interactions
Equations of motion
Molecular dynamics
Synchronization
Data storage equipment
synchronism
Atoms
equations of motion
electrostatics
molecular dynamics
scaling
atoms
interactions

ASJC Scopus subject areas

  • Computer Science Applications
  • Physics and Astronomy(all)

Cite this

Communications overlapping in fast multipole particle dynamics methods. / Kurzak, Jakub; Pettitt, Bernard.

In: Journal of Computational Physics, Vol. 203, No. 2, 01.03.2005, p. 731-743.

Research output: Contribution to journalArticle

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