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.

• Type: Conference
• Year: 2003
• Where: ICCS
• Authors: Laxmikant V. Kalé, Sameer Kumar, Gengbin Zheng, Chee Wai Lee
• Keywords: ICCS 2003, Multiple Interacting Performance, Study Involving Namd, Tera-FLOPS Level Performance