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

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.

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.

@INPROCEEDINGS{namdPerfStudy,
	author = "Laxmikant V. Kal{\'e} and Sameer Kumar and Gengbin Zheng and Chee Wai Lee",
	title = "Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study",
	booktitle = "Terascale Performance Analysis Workshop, International Conference on Computational Science(ICCS)",
	month = "June",
	year = "2003",
	address = "Melbourne, Australia",
	group = Y,
}