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
A system for interactive molecular dynamics simulation
I3D '01 Proceedings of the 2001 symposium on Interactive 3D graphics
A Parallel-Object Programming Model for PetaFLOPS Machines and Blue Gene/Cyclops
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
Emulating PetaFLOPS Machines and Blue Gene
IPDPS '01 Proceedings of the 15th International Parallel & Distributed Processing Symposium
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
Parallelizing a DNA Simulation Code for the Cray MTA-2
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Blue Gene: a vision for protein science using a petaflop supercomputer
IBM Systems Journal - Deep computing for the life sciences
An orchestration language for parallel objects
LCR '04 Proceedings of the 7th workshop on Workshop on languages, compilers, and run-time support for scalable systems
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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.