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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++doi:10.1145/2063384.2063466 dblp:conf/sc/MeiSZBKPH11 fatcat:jgkzpijiljgl3hxfhl2vevglyu