Efficient parallelization of molecular dynamics simulations with short-ranged forces
Efficient parallelization of molecular dynamics simulations with short-ranged forces
复制标题
短程力分子动力学模拟的高效并行化
DOI：
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发表时间：
2014
期刊：
影响因子：
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通讯作者：
R. Meyer
中科院分区：
文献类型：
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作者：
R. Meyer
最近，一种替代策略的并行化的分子动力学模拟与短程力已被提出。在这项工作中，使用三种类型的基准模拟在各种多核系统上测试了该算法。结果表明，新算法给出了一致的加速比，这取决于模拟系统的属性，无论是可比的或上级与空间分解得到的。在不同系统上的并行加速比的比较表明，在多核机器上，该方法的并行效率主要受存储器访问速度的限制。
Recently, an alternative strategy for the parallelization of molecular dynamics simulations with short-ranged forces has been proposed. In this work, this algorithm is tested on a variety of multi-core systems using three types of benchmark simulations. The results show that the new algorithm gives consistent speedups which are depending on the properties of the simulated system either comparable or superior to those obtained with spatial decomposition. Comparisons of the parallel speedup on different systems indicates that on multi-core machines the parallel efficiency of the method is mainly limited by memory access speed.