Paper Citing NAMD - Abstract
Kale, L.V.; Kumar, S.; Zheng, G.B.; Lee, C.W.
Scaling molecular dynamics to 3000 processors with projections: A performance analysis case study
COMPUTATIONAL SCIENCE - ICCS 2003, PT IV, PROCEEDINGS, 2660:23-32, 2003
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.
