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.
You can also create your personal schedule on the SC11 app (Boopsie) on your smartphone. Simply select a session you want to attend and "add" it to your plan. Continue in this manner until you have created your own personal schedule. All your events will appear under "My Event Planner" on your smartphone.
Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime
SESSION: Molecular Dynamics and Computational Physics
EVENT TYPE: Paper
TIME: 11:00AM - 11:30AM
AUTHOR(S):Chao Mei, Yanhua Sun, Gengbin Zheng, James C. Phillips, Eric J. Bohm, Chris Harrison, Laxmikant V. Kale
ABSTRACT: A 100-million-atom biomolecular simulation with NAMD is one of the three benchmarks for the NSF-funded sustainable petascale machine. Simulating this
large molecular system on a petascale machine presents great challenges, including handling I/O, large memory footprint and getting good strong-scaling
results. In this paper, we present parallel I/O techniques to enable the simulation. A new SMP model is designed to efficiently utilize ubiquitous wide multicore clusters by extending the Charm++ asynchronous message-driven
runtime. We exploit node-aware techniques to optimize both the application and the underlying SMP runtime. Hierarchical load balancing is further exploited to scale NAMD to the full Jaguar PF Cray XT5 (224,076 cores) at Oak Ridge National Laboratory, both with and without PME full electrostatics, achieving 93% parallel efficiency (vs 6720 cores) at 9ms per step for a simple cutoff calculation.
Excellent scaling is also obtained on 65,536 cores of the Intrepid Blue Gene/P at Argonne National Laboratory.
Chao Mei - University of Illinois at Urbana-Champaign
Yanhua Sun - University of Illinois at Urbana-Champaign
Gengbin Zheng - University of Illinois at Urbana-Champaign
James C. Phillips - University of Illinois at Urbana-Champaign
Eric J. Bohm - University of Illinois at Urbana-Champaign
Chris Harrison - University of Illinois at Urbana-Champaign
Laxmikant V. Kale - University of Illinois at Urbana-Champaign