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

George S. Almasi, Câlin Caşcaval, José G. Castaños, Monty Denneau, Wilm Donath, Maria Eleftheriou, Mark Giampapa, Howard Ho, Derek Lieber, José E. Moreira, Dennis Newns, Marc Snir, Henry S. Warren

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)317-351
Number of pages35
JournalInternational Journal of Parallel Programming
Issue number4
StatePublished - Aug 2002
Externally publishedYes


  • Cellular architecture
  • Massively parallel computing
  • Molecular dynamics
  • Performance evaluation

ASJC Scopus subject areas

  • Software
  • Theoretical Computer Science
  • Information Systems


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