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. © Springer-Verlag Berlin Heidelberg 2003.
CITATION STYLE
Kalé, L. V., Kumar, S., Zheng, G., & Lee, C. W. (2003). Scaling molecular dynamics to 3000 processors with projections: A performance analysis case study. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2660, 23–32. https://doi.org/10.1007/3-540-44864-0_3
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