Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kalé,
James C. Phillips, and Chris Harrison.
Enabling and scaling biomolecular simulations of 100 million atoms on
petascale machines with a multicore-optimized message-driven runtime.
In Proceedings of the 2011 ACM/IEEE conference on
Supercomputing, pp. 61:1-61:11, Seattle, WA, November 2011.
MEI2011-LK
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.
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