首页> 外文会议>Parallel and Distributed Processing and Applications; Lecture Notes in Computer Science; 4330 >Parallelization Algorithms for Three-Body Interactions in Molecular Dynamics Simulation
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Parallelization Algorithms for Three-Body Interactions in Molecular Dynamics Simulation

机译:分子动力学模拟中三体相互作用的并行化算法

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Two force decomposition algorithms are proposed for parallelizing three-body interactions in Molecular Dynamics (MD) simulations. The first algorithm divides the entire 3D force matrix into equal sized force cubes that are assigned to parallel processors. In the second strategy, the force matrix is decomposed into slices of two-dimensional force matrixes, and those slices are distributed among processors cyclically. The proposed decomposition algorithms are implemented using MPI and tested in computational experiments. The performances of proposed decomposition methods are studied and compared with computational load theoretical analysis. Both theoretical prediction and computation experiments demonstrate that the load balance is a key factor that impacts the parallel performance of the examined system, and the cyclic force decomposition algorithm produced reasonably good overall performances.
机译:提出了两种力分解算法,用于并行化分子动力学(MD)模拟中的三体相互作用。第一种算法将整个3D力矩阵分为相等大小的力立方体,这些立方体被分配给并行处理器。在第二种策略中,力矩阵被分解为二维力矩阵的切片,并且这些切片循环地分布在处理器之间。提出的分解算法是使用MPI实现的,并在计算实验中进行了测试。研究了所提出的分解方法的性能,并与计算负荷理论分析进行了比较。理论预测和计算实验均表明,负载平衡是影响所检查系统的并行性能的关键因素,而循环力分解算法可产生相当好的整体性能。

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