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Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation
| James Phillips | Yanhua Sun | Nikhil Jain | Eric Bohm | Laxmikant Kale
International Conference for High Performance Computing, Networking, Storage and Analysis (SC) 2014
Publication Type: Paper
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Abstract
Currently deployed petascale supercomputers typically 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 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, and ANL Mira.
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