Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation

James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, Laxmikant V Kale

Research output: Contribution to journalConference article

Abstract

Currently deployed petascale supercomputers typically use toroidal network topologies in three or more dimensions. While these networks perform well for topology-agnostic codes on a few thousand nodes, leadership machines with 20,000 nodes require topology awareness to avoid network contention for communication-intensive codes. Topology adaptation is complicated by irregular node allocation shapes and holes due to dedicated input/output nodes or hardware failure. In the context of the popular molecular dynamics program NAMD, we present methods for mapping a periodic 3-D grid of fixed-size spatial decomposition domains to 3-D Cray Gemini and 5-D IBM Blue Gene/Q toroidal networks to enable hundred-million atom full machine simulations, and to similarly partition node allocations into compact domains for smaller simulations using multiple copy algorithms. Additional enabling techniques are discussed and performance is reported for NCSA Blue Waters, ORNL Titan, ANL Mira, TACC Stampede, and NERSC Edison.

Original languageEnglish (US)
Article number7012994
Pages (from-to)81-91
Number of pages11
JournalInternational Conference for High Performance Computing, Networking, Storage and Analysis, SC
Volume2015-January
Issue numberJanuary
DOIs
StatePublished - Jan 16 2014
EventInternational Conference for High Performance Computing, Networking, Storage and Analysis, SC 2014 - New Orleans, United States
Duration: Nov 16 2014Nov 21 2014

ASJC Scopus subject areas

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

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