title: Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.
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.
authors.forename: James C
authors.initials: JC
authors.lastname: Phillips
authors.forename: Yanhua
authors.initials: Y
authors.lastname: Sun
authors.forename: Nikhil
authors.initials: N
authors.lastname: Jain
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Bohm
authors.forename: Laxmikant V
authors.initials: LV
authors.lastname: Kalé