@inbook{89da7cde791c4bf6907351c4bda4fbf6,
title = "Scaling molecular dynamics to 3000 processors with projections: A performance analysis case study",
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.",
author = "Kal{\'e}, {Laxmikant V.} and Sameer Kumar and Gengbin Zheng and Lee, {Chee Wai}",
year = "2003",
doi = "10.1007/3-540-44864-0_3",
language = "English (US)",
isbn = "3540401970",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer",
pages = "23--32",
editor = "Sloot, {Peter M. A.} and David Abramson and Bogdanov, {Alexander V.} and Gorbachev, {Yuriy E.} and Dongarra, {Jack J.} and Zomaya, {Albert Y.}",
booktitle = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
address = "Germany",
}