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SCHEDULE: NOV 16-21, 2014
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Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation
SESSION: Heterogeneity and Scaling in Applications
EVENT TYPE: Papers
TIME: 11:00AM - 11:30AM
SESSION CHAIR: Justin Luitjens
AUTHOR(S):James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, Laxmikant V. Kale
ROOM:393-94-95
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
on 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.
Chair/Author Details:
Justin Luitjens (Chair) - NVIDIA Corporation
James C. Phillips - University of Illinois at Urbana-Champaign
Yanhua Sun - University of Illinois at Urbana-Champaign
Nikhil Jain - University of Illinois at Urbana-Champaign
Eric J. Bohm - University of Illinois at Urbana-Champaign
Laxmikant V. Kale - University of Illinois at Urbana-Champaign
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