Scalable molecular dynamics for large biomolecular systems

Article type: Research Article

Authors: Brunner, Robert K. | Phillips, James C. | Kal\'e, Laxmikant V.

Affiliations: Theoretical Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. E-mail: {rbrunner,jcphill}@uiuc.edu | Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. E-mail: [email protected]

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.

Journal: Scientific Programming, vol. 8, no. 3, pp. 195-207, 2000