A Cyclic Force Decomposition Algorithm for Parallelising Three-Body Interactions in Molecular Dynamics Simulations

Jianhui Li, Zhongwu Zhou, R. Sadus
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引用次数: 8

Abstract

A cyclic force decomposition algorithm is examined for parallelising three body interactions. The algorithm is based on the decomposition of a 3D force matrix into slices of 2D force matrixes in cyclic task assignments. The proposed decomposition algorithm is implemented using MPI and tested in computational experiments of MD simulations. The performance of the decomposition method is studied in terms of load balance, achieved speedup and parallel efficiency. Theoretical analysis of effective triplets is proposed and conducted by which load balance status can be predicted and compared with benchmark measurements. Reasonably good overall performance is achieved with the proposed algorithm. Both theoretical analysis and computation experiments demonstrate that the load balance is a key factor that impacts the parallel efficiency of the system examined in this study
分子动力学模拟中并行化三体相互作用的循环力分解算法
研究了三体相互作用并行化的循环力分解算法。该算法基于在循环任务分配中将三维力矩阵分解为二维力矩阵的切片。利用MPI实现了该分解算法,并在MD仿真计算实验中进行了验证。从负载平衡的角度研究了该分解方法的性能,实现了加速和并行效率。提出并进行了有效三元组的理论分析,通过有效三元组可以预测负载平衡状态,并与基准测量结果进行比较。提出的算法取得了较好的综合性能。理论分析和计算实验均表明,负载平衡是影响本研究系统并行效率的关键因素
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