FAST PARALLEL ALGORITHMS FOR SHORT-RANGE MOLECULAR-DYNAMICS
FAST PARALLEL ALGORITHMS FOR SHORT-RANGE MOLECULAR-DYNAMICS
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DOI：
10.1006/jcph.1995.1039
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发表时间：
1995-03-01
影响因子：
4.1
通讯作者：
PLIMPTON, S
中科院分区：
文献类型：
--
作者：
PLIMPTON, S
提出了经典分子动力学的三种并行算法。第一种算法为每个处理器分配一个固定的原子子集；第二种算法为每个处理器分配一个固定的原子间作用力子集进行计算；第三种算法为每个处理器分配一个固定的空间区域，这些算法适用于难以有效并行化的分子动力学模型-那些具有短程作用力的模型，其中每个原子的邻居快速变化，它们可以在任何允许独立执行的处理器之间传递数据的分布式内存并行机上实现。这些算法在标准的Lennard-Jones基准问题上进行了测试，系统大小从500到100,000,000个原子，在几台并行超级计算机上进行了测试-Ncube 2，Intel iPSC/860和Paragon，以及Cray T3D。将结果与已报道的最快的矢量化Gray Y-MP和C90算法进行比较，结果表明，当前一代的并行机即使在小问题上也能与传统的向量超级计算机竞争，对于大问题，空间算法的并行效率达到90%，1840节点的Intel Paragon处理器的执行速度比单个Gray C90处理器快165。还讨论了三种算法之间的权衡以及使它们适应更复杂的分子动力学模拟的指导方针。(C)1995年学术出版社。
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 Gray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems, for large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Gray C90 processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed. (C) 1995 Academic Press, Inc.