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PRODID:-//Microsoft Corporation//Outlook MIMEDIR//EN
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DTSTART:20111117T190000Z
DTEND:20111117T193000Z
LOCATION:TCC 304
DESCRIPTION;ENCODING=QUOTED-PRINTABLE:ABSTRACT: A 100-million-atom biomolecular simulation with NAMD is one of the three benchmarks for the NSF-funded sustainable petascale machine. Simulating this=0Alarge molecular system on a petascale machine presents great challenges, including handling I/O, large memory footprint and getting good strong-scaling=0Aresults. 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=0Aruntime. 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 9ms per step for a simple cutoff calculation.=0AExcellent scaling is also obtained on 65,536 cores of the Intrepid Blue Gene/P at Argonne National Laboratory.
SUMMARY:Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime
PRIORITY:3
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