NAMD: Biomolecular Simulation on Thousands of Processors
International Conference for High Performance Computing, Networking, Storage and Analysis (SC) 2002
Publication Type: Paper
NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC 2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demontrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place on MPI by the Charm++/Converse parallel runtime system.
James C. Phillips and Gengbin Zheng and Sameer Kumar and Laxmikant V. Kale, "NAMD: Biomolecular Simulation on Thousands of Processors", Proceedings of the 2002 ACM/IEEE conference on Supercomputing, Baltimore, MD, pp. 1-18, September, 2002.