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Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation
| Citations: | 2 - 1 self |
BibTeX
@MISC{Phillips_mappingto,
author = {James C. Phillips and Yanhua Sun and Nikhil Jain and Eric J. Bohm and Laximant V. Kalé},
title = {Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation},
year = {}
}
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Abstract
Abstract — Currently deployed petascale supercomputers typ-ically use toroidal network topologies in three to five 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 com-plicated 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, and ANL Mira.
Keyphrases
petascale biomolecular simulation irregular torus topology input output node abstract currently leadership machine 5-d ibm blue gene 3-d cray gemini ncsa blue water hundred-million atom full machine simulation hardware failure irregular node allocation shape topology awareness popular molecular dynamic program namd anl mira periodic 3-d grid petascale supercomputer additional enabling technique ornl titan communication-intensive code multiple-copy algorithm topology-agnostic code network contention topology adaptation fixed-size spatial decomposition domain compact domain partition node allocation toroidal network topology
