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Phillips JC, Sun Y, Jain N, et al. Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. SC Conf Proc. 2014;2014:81-91doi: 10.1109/SC.2014.12.
Phillips, J. C., Sun, Y., Jain, N., Bohm, E. J., & Kalé, L. V. (2014). Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. SC ... conference proceedings. SC (Conference : Supercomputing), 201481-91. https://doi.org/10.1109/SC.2014.12
Phillips, James C, et al. "Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation." SC ... conference proceedings. SC (Conference : Supercomputing) vol. 2014 (2014): 81-91. doi: https://doi.org/10.1109/SC.2014.12
Phillips JC, Sun Y, Jain N, Bohm EJ, Kalé LV. Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. SC Conf Proc. 2014;2014:81-91. doi: 10.1109/SC.2014.12. PMID: 25594075; PMCID: PMC4292797.
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SC Conf Proc. 2014;2014:81-91. doi: 10.1109/SC.2014.12.

Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.

SC ... conference proceedings. SC (Conference : Supercomputing)

James C Phillips, Yanhua Sun, Nikhil Jain, Eric J Bohm, Laxmikant V Kalé

PMID: 25594075 PMCID: PMC4292797 DOI: 10.1109/SC.2014.12

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 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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