Scalable Molecular Dynamics for Large Biomolecular Systems
| Robert Brunner | James Phillips | Laxmikant Kale
International Conference for High Performance Computing, Networking, Storage and Analysis (SC) 2000
Publication Type: Paper
Repository URL: namdSC2000
Abstract
We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.
TextRef
Robert K. Brunner and James C. Phillips and Laxmikant V. Kale, "Scalable Molecular Dynamics for Large Biomolecular Systems", Proceedings of Supercomputing (SC) 2000, Dallas, TX, November 2000. Nominated for Gordon Bell Award.
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