Article

International Journal of Parallel Programming

, Volume 30, Issue 4, pp 317-351

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

  • George S. Almasi
  • , Călin Caşcaval
  • , José G. Castaños
  • , Monty DenneauAffiliated withIBM Thomas J. Watson Research Center
  • , Wilm DonathAffiliated withIBM Thomas J. Watson Research Center
  • , Maria EleftheriouAffiliated withIBM Thomas J. Watson Research Center
  • , Mark GiampapaAffiliated withIBM Thomas J. Watson Research Center
  • , Howard HoAffiliated withIBM Thomas J. Watson Research Center
  • , Derek LieberAffiliated withIBM Thomas J. Watson Research Center
    • , José E. MoreiraAffiliated withIBM Thomas J. Watson Research Center
    • , Dennis NewnsAffiliated withIBM Thomas J. Watson Research Center
    • , Marc SnirAffiliated withIBM Thomas J. Watson Research Center
    • , Henry S. WarrenJr.Affiliated withIBM Thomas J. Watson Research Center

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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 computing molecular dynamics performance evaluation cellular architecture