Name
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 cutoffelectrostatics 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. |
Year | DOI | Venue |
|---|---|---|
2002 | 10.1109/SC.2002.10019 | SC |
Keywords | Field | DocType |
high performance simulation,order n log,large biomolecular system,asci red machine,quadrics elan library,similar scaling,psc lemieux alpha cluster,aggressive measurement-based predictive load,converse parallel runtime system,biomolecular simulation code,scientific visualization,membrane protein,computational modeling,visual cues,perception,water soluble,simulation model,nucleic acid,molecular dynamic,field lines,scalability,particle accelerators,volume rendering,parallel computer,production systems,load balance,lipid bilayer,texture mapping,small angle x ray scattering,computer simulation,electrostatics,high performance computing,lipidomics,object oriented design | Particle Mesh,Supercomputer,Computer science,Load balancing (computing),Parallel computing,Multiprocessing,Time complexity,Runtime system,Scalability,SC2000 | Conference |
ISSN | ISBN | Citations |
1063-9535 | 978-0-7695-1524-3 | 114 |
PageRank | References | Authors |
10.80 | 8 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| James C. Phillips | 1 | 1376 | 147.18 |
| Gengbin Zheng | 2 | 829 | 55.03 |
| Sameer Kumar | 3 | 160 | 14.39 |
| Laxmikant V. Kale | 4 | 2871 | 248.18 |