Live Webcast 15th Annual Charm++ Workshop

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 \charmpp{} 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 9\,ms 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.