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PRODID:-//Microsoft Corporation//Outlook MIMEDIR//EN
VERSION:1.0
BEGIN:VEVENT
DTSTART:20141118T170000Z
DTEND:20141118T173000Z
LOCATION:393-94-95
DESCRIPTION;ENCODING=QUOTED-PRINTABLE:ABSTRACT: Currently deployed petascale supercomputers typically use toroidal network=0Atopologies in three or more dimensions.  While these networks perform well=0Afor topology-agnostic codes on a few thousand nodes, leadership machines=0Awith 20,000 nodes require topology awareness to avoid network contention=0Aon communication-intensive codes.  Topology adaptation is complicated by=0Airregular node allocation shapes and holes due to dedicated input/output=0Anodes or hardware failure.  In the context of the popular molecular=0Adynamics program NAMD, we present methods for mapping a periodic 3-D grid=0Aof fixed-size spatial decomposition domains to 3-D Cray Gemini and 5-D IBM=0ABlue Gene/Q toroidal networks to enable hundred-million atom full machine=0Asimulations, and to similarly partition node allocations into compact=0Adomains for smaller simulations using multiple-copy algorithms.=0AAdditional enabling techniques are discussed and performance is reported=0Afor NCSA Blue Waters, ORNL Titan, ANL Mira, TACC Stampede, and NERSC Edison.
SUMMARY:Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation
PRIORITY:3
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