CHARM++: a portable concurrent object oriented system based on C++
OOPSLA '93 Proceedings of the eighth annual conference on Object-oriented programming systems, languages, and applications
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines
IEEE Computational Science & Engineering
NAMD: A Case Study in Multilingual Parallel Programming
LCPC '97 Proceedings of the 10th International Workshop on Languages and Compilers for Parallel Computing
Adapting to Load on Workstation Clusters
FRONTIERS '99 Proceedings of the The 7th Symposium on the Frontiers of Massively Parallel Computation
A portable distributed implementation of the parallel multipole tree algorithm
HPDC '95 Proceedings of the 4th IEEE International Symposium on High Performance Distributed Computing
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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.