sponsored byIEEEACMThe International Conference for High Performance 
Computing, Networking, Storage and Analysis
FacebookTwitterGoogle PlusLinkedInYouTubeFlickr

SCHEDULE: NOV 16-21, 2014

When viewing the Technical Program schedule, on the far righthand side is a column labeled "PLANNER." Use this planner to build your own schedule. Once you select an event and want to add it to your personal schedule, just click on the calendar icon of your choice (outlook calendar, ical calendar or google calendar) and that event will be stored there. As you select events in this manner, you will have your own schedule to guide you through the week.

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

SESSION: Heterogeneity and Scaling in Applications


TIME: 11:00AM - 11:30AM

SESSION CHAIR: Justin Luitjens

AUTHOR(S):James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, Laxmikant V. Kale



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
on 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.

Chair/Author Details:

Justin Luitjens (Chair) - NVIDIA Corporation

James C. Phillips - University of Illinois at Urbana-Champaign

Yanhua Sun - University of Illinois at Urbana-Champaign

Nikhil Jain - University of Illinois at Urbana-Champaign

Eric J. Bohm - University of Illinois at Urbana-Champaign

Laxmikant V. Kale - University of Illinois at Urbana-Champaign

Add to iCal  Click here to download .ics calendar file

Add to Outlook  Click here to download .vcs calendar file

Add to Google Calendarss  Click here to add event to your Google Calendar

Paper provided by the ACM Digital Library

Paper also available from IEEE Computer Society