Communications overlapping in fast multipole particle dynamics methods

  • Authors:

  • Jakub Kurzak;B. Montgomery Pettitt

  • Affiliations:

  • Department of Computer Science, University of Houston, Houston, TX 77204-5003, USA;Department of Computer Science, University of Houston, Houston, TX 77204-5003, USA and Department of Chemistry, University of Houston, 4800 Calhoun, Houston, TX 77204, USA

  • Venue:
  • Journal of Computational Physics
  • Year:
  • 2005

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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.