Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6

Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, James C. Phillips, Laximant V. Kalé, Terry R. Jones

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Achieving good scaling for fine-grained communication intensive applications on modern supercomputers remains challenging. In our previous work, we have shown that such an application - NAMD - scales well on the full Jaguar XT5 without long-range interactions; Yet, with them, the speedup falters beyond 64K cores. Although the new Gemini interconnect on Cray XK6 has improved network performance, the challenges remain, and are likely to remain for other such networks as well. We analyze communication bottlenecks in NAMD and its CHARM++ runtime, using the Projections performance analysis tool. Based on the analysis, we optimize the runtime, built on the uGNI library for Gemini. We present several techniques to improve the fine-grained communication. Consequently, the performance of running 92224-atom Apoa1 with GPUs on TitanDev is improved by 36%. For 100-million-atom STMV, we improve upon the prior Jaguar XT5 result of 26 ms/step to 13 ms/step using 298,992 cores on Jaguar XK6.

Original languageEnglish (US)
Title of host publication2012 International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2012
DOIs
StatePublished - Dec 1 2012
Event2012 24th International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2012 - Salt Lake City, UT, United States
Duration: Nov 10 2012Nov 16 2012

Publication series

NameInternational Conference for High Performance Computing, Networking, Storage and Analysis, SC
ISSN (Print)2167-4329
ISSN (Electronic)2167-4337

Other

Other2012 24th International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2012
CountryUnited States
CitySalt Lake City, UT
Period11/10/1211/16/12

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Computer Science Applications
  • Hardware and Architecture
  • Software

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