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Journal of Mathematical Chemistry

, Volume 45, Issue 2, pp 503–512 | Cite as

Communication performance of d-meshes in molecular dynamics simulation

  • Roman Trobec
  • Urban Borštnik
  • Dušanka Janežič
Original Paper

Abstract

Communication algorithms, tailored for molecular dynamics simulation on d-meshes, are evaluated in terms of communication efficiency. It has been shown elsewhere that d-meshes are better than other regular topologies, e.g., hypercubes and standard toroidal 4-meshes, when compared in their diameter and average distance among nodes. Collective communication is needed in molecular dynamics simulation for the distribution of coordinates and calculation and distribution of new energies. We show that both collective communication patterns used in molecular dynamics can be efficiently solved with congestion-free algorithms for all-to-all communication based on store-and-forward routing and routing tables. Our results indicate that d-meshes compete with hypercubes in parallel computers. Therefore d-meshes can also be used as a communication upgrade of existing molecular dynamics simulation platforms and can be successfully applied to perform fast molecular dynamics simulation.

Keywords

d-meshes Parallel molecular dynamics simulation Computer interconnection topologies 

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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Roman Trobec
    • 1
  • Urban Borštnik
    • 2
  • Dušanka Janežič
    • 2
  1. 1.Jožef Stefan InstitutLjubljanaSlovenia
  2. 2.National Institute of ChemistryLjubljanaSlovenia

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