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Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime
2011
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '11
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