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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Phillips, J.C. Gengbin Zheng Kumar, S. Kale, L.V. |
| Copyright Year | 2002 |
| Description | Author affiliation: University of Illinois at Urbana-Champaign (Phillips, J.C.) |
| 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. |
| Starting Page | 36 |
| Ending Page | 36 |
| File Size | 333782 |
| Page Count | 1 |
| File Format | |
| ISBN | 076951524X |
| ISSN | 10639535 |
| DOI | 10.1109/SC.2002.10019 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2002-11-16 |
| Publisher Place | USA |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Object oriented modeling Computational modeling Electrostatics Force measurement Scalability Lipidomics Equations Solvents Computer simulation Production systems |
| Content Type | Text |
| Resource Type | Article |
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