International Journal of Parallel Programming

, Volume 30, Issue 4, pp 317–351

Demonstrating the Scalability of a Molecular Dynamics Application on a Petaflops Computer

Authors

  • George S. Almasi
  • Călin Caşcaval
  • José G. Castaños
  • Monty Denneau
    • IBM Thomas J. Watson Research Center
  • Wilm Donath
    • IBM Thomas J. Watson Research Center
  • Maria Eleftheriou
    • IBM Thomas J. Watson Research Center
  • Mark Giampapa
    • IBM Thomas J. Watson Research Center
  • Howard Ho
    • IBM Thomas J. Watson Research Center
  • Derek Lieber
    • IBM Thomas J. Watson Research Center
  • José E. Moreira
    • IBM Thomas J. Watson Research Center
  • Dennis Newns
    • IBM Thomas J. Watson Research Center
  • Marc Snir
    • IBM Thomas J. Watson Research Center
  • Henry S. WarrenJr.
    • IBM Thomas J. Watson Research Center
Article

DOI: 10.1023/A:1019856029918

Cite this article as:
Almasi, G.S., Caşcaval, C., Castaños, J.G. et al. International Journal of Parallel Programming (2002) 30: 317. doi:10.1023/A:1019856029918
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Abstract

The IBM Blue Gene/C parallel computer aims to demonstrate the feasibility of a cellular architecture computer with millions of concurrent threads of execution. One of the major challenges in this project is showing that applications can successfully scale to this massive amount of parallelism. In this paper we demonstrate that the simulation of protein folding using classical molecular dynamics falls in this category. Starting from the sequential version of a well known molecular dynamics code, we developed a new parallel implementation that exploited the multiple levels of parallelism present in the Blue Gene/C cellular architecture. We performed both analytical and simulation studies of the behavior of this application when executed on a very large number of threads. As a result, we demonstrate that this class of applications can execute efficiently on a large cellular machine.

Massively parallel computingmolecular dynamicsperformance evaluationcellular architecture

Copyright information

© Plenum Publishing Corporation 2002