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Progress in Scaling Biomolecular Simulations to Petaflop Scale Platforms

  • Blake G. Fitch
  • Aleksandr Rayshubskiy
  • Maria Eleftheriou
  • T. J. Christopher Ward
  • Mark Giampapa
  • Michael C. Pitman
  • Robert S. Germain
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4375)

Abstract

This paper describes some of the issues involved with scaling biomolecular simulations onto massively parallel machines drawing on the Blue Matter application team’s experiences with Blue Gene/L. Our experiences in scaling biomolecular simulation to one atom/node on BG/L should be relevant to scaling biomolecular simulations onto larger peta-scale platforms because the path to increased performance is through the exploitation of increased concurrency so that even larger systems will have to operate in the extreme strong scaling regime. Petascale platforms also present challenges with regard to the correctness of biomolecular simulations since longer time-scale simulations are more likely to encounter significant energy drift. Total energy drift data for a microsecond-scale simulation is presented along with the measured scalability of various components of a molecular dynamics time-step.

Keywords

Molecular Dynamic Molecular Simulation Replica Exchange Replica Exchange Molecular Dynamic Strong Scaling 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Blake G. Fitch
    • 1
  • Aleksandr Rayshubskiy
    • 1
  • Maria Eleftheriou
    • 1
  • T. J. Christopher Ward
    • 2
  • Mark Giampapa
    • 1
  • Michael C. Pitman
    • 1
  • Robert S. Germain
    • 1
  1. 1.IBM Thomas J. Watson Research Center, 1101 Kitchawan Road/Route 134, Yorktown Heights, NY 10598USA
  2. 2.IBM Hursley Park, Hursley, Hursley SO212JNUK

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