Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study

  • Laxmikant V. Kalé
  • Sameer Kumar
  • Gengbin Zheng
  • Chee Wai Lee
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2660)

Abstract

Some of the most challenging applications to parallelize scalably are the ones that present a relatively small amount of computation per iteration. Multiple interacting performance challenges must be identified and solved to attain high parallel efficiency in such cases. We present a case study involving NAMD, a parallel molecular dynamics application, and efforts to scale it to run on 3000 processors with Tera-FLOPS level performance. NAMD is implemented in Charm++, and the performance analysis was carried out using “projections”, the performance visualization/analysis tool associated with Charm++. We will showcase a series of optimizations facilitated by projections. The resultant performance of NAMD led to a Gordon Bell award at SC2002.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Laxmikant V. Kalé
    • 1
  • Sameer Kumar
    • 1
  • Gengbin Zheng
    • 1
  • Chee Wai Lee
    • 1
  1. 1.Department of Computer ScienceUniversity of Illinois at Urbana-ChampaignUSA

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