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Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study
Workshop on Terascale Performance Analysis at ICCS 2003
Publication Type: Paper
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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.
TextRef
Laxmikant V. Kale and Sameer Kumar and Gengbin Zheng and Chee Wai Lee, "Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study", Terascale Performance Analysis Workshop, International Conference on Computational Science(ICCS), Melbourne, Australia, June 2003.
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