James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laximant V.
Kalé.
Mapping to irregular torus topologies and other techniques for
petascale biomolecular simulation.
In Proceedings of the International Conference on High
Performance Computing, Networking, Storage and Analysis, SC '14, pp. 81-91.
IEEE Press, 2014.
(PMC: PMC4292797)
PHIL2014-LK
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.
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