NAMD: Biomolecular Simulation on Thousands of Processors
- 1 January 2002
- conference paper
- Published by Institute of Electrical and Electronics Engineers (IEEE)
- Vol. 1800 (10639535) , 36
- https://doi.org/10.1109/sc.2002.10019
Abstract
NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.Keywords
This publication has 11 references indexed in Scilit:
- The Quadrics network: high-performance clustering technologyIEEE Micro, 2002
- A system for interactive molecular dynamics simulationPublished by Association for Computing Machinery (ACM) ,2001
- Scalable Molecular Dynamics for Large Biomolecular SystemsPublished by Institute of Electrical and Electronics Engineers (IEEE) ,2000
- NAMD2: Greater Scalability for Parallel Molecular DynamicsJournal of Computational Physics, 1999
- Adapting to load on workstation clustersPublished by Institute of Electrical and Electronics Engineers (IEEE) ,1999
- A new parallel method for molecular dynamics simulation of macromolecular systemsJournal of Computational Chemistry, 1996
- Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systemsThe Journal of Chemical Physics, 1993
- A Partitioning Strategy for Nonuniform Problems on MultiprocessorsIEEE Transactions on Computers, 1987
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983
- AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactionsJournal of Computational Chemistry, 1981