Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized Message-driven runtime

Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kale, James C.phillips, Chris Harrison

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

Abstract

A 100-million-atom biomolecular simulation with NAMD is one of the three benchmarks for the NSF-funded sustainable petascale machine. Simulating this large molecular system on a petascale machine presents great challenges, including handling I/O, large memory footprint and getting good strong-scaling results. In this paper, we present parallel I/O techniques to enable the simulation. A new SMP model is designed to efficiently utilize ubiquitous wide multicore clusters by extending the CHARM++ asynchronous message-driven runtime. We exploit node-aware techniques to optimize both the application and the underlying SMP runtime. Hierarchical load balancing is further exploited to scale NAMD to the full Jaguar PF Cray XT5 (224,076 cores) at Oak Ridge National Laboratory, both with and without PME full electrostatics, achieving 93% parallel efficiency (vs 6720 cores) at 9 ms per step for a simple cutoff calculation. Excellent scaling is also obtained on 65,536 cores of the Intrepid Blue Gene/P at Argonne National Laboratory.

Original languageEnglish (US)
Title of host publicationProceedings of 2011 SC - International Conference for High Performance Computing, Networking, Storage and Analysis
DOIs
StatePublished - 2011
Event2011 International Conference for High Performance Computing, Networking, Storage and Analysis, SC11 - Seattle, WA, United States
Duration: Nov 12 2011Nov 18 2011

Publication series

NameProceedings of 2011 SC - International Conference for High Performance Computing, Networking, Storage and Analysis

Other

Other2011 International Conference for High Performance Computing, Networking, Storage and Analysis, SC11
CountryUnited States
CitySeattle, WA
Period11/12/1111/18/11

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Computer Science Applications

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