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Fast Parallel Algorithms for Short-Range Molecular Dynamics (1995)
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| Venue: | JOURNAL OF COMPUTATIONAL PHYSICS |
| Citations: | 653 - 7 self |
BibTeX
@ARTICLE{Plimpton95fastparallel,
author = {Steve Plimpton},
title = { Fast Parallel Algorithms for Short-Range Molecular Dynamics},
journal = {JOURNAL OF COMPUTATIONAL PHYSICS},
year = {1995},
volume = {117},
pages = {1--19}
}
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Abstract
Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently -- those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed--memory parallel machine which allows for message--passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers -- the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventi...
Keyphrases
fast parallel algorithm short-range molecular dynamic fixed subset standard lennard-jones benchmark problem current generation message passing classical molecular dynamic molecular dynamic model parallel machine inter-atomic force system size atom change c90 algorithm fixed spatial region second assigns short-range force distributed memory parallel machine parallel algorithm vectorized cray y-mp cray t3d third assigns several parallel supercomputer
