Scalable Molecular Dynamics for Large Biomolecular Systems

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.

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.

@inproceedings{ScalableMolSC00,
  author = "Robert K. Brunner and James C. Phillips and Laxmikant V. Kale",
  title = "{Scalable Molecular Dynamics for Large Biomolecular Systems}",
  booktitle = "Proceedings of Supercomputing (SC) 2000, Dallas, TX, November 2000.  Nominated for Gordon Bell Award.",
  year = "2000",
  month = "November"
}