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首页> 外文会议>International Conference on High Performance Computing >A Novel Force Matrix Transformation with Optimal Load-Balance for 3-Body Potential Based Parallel Molecular Dynamics Using Atom-Decomposition in a Heterogeneous Cluster Environment
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A Novel Force Matrix Transformation with Optimal Load-Balance for 3-Body Potential Based Parallel Molecular Dynamics Using Atom-Decomposition in a Heterogeneous Cluster Environment

机译：一种新的力矩阵变换，具有在异构群环境中使用原子分解的基于3体潜在的平行分子动态的最佳负载平衡

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摘要

Evaluating the Force Matrix constitutes the most computationally intensive part of a Molecular Dynamics (MD) simulation. In three-body MD simulations, the total energy of the system is determined by the energy of every unique triple in the system and the force matrix is three-dimensional. The execution time of a three-body MD algorithm is thus proportional to the cube of the number of atoms in the system. Fortunately, there exist symmetries in the Force Matrix that can be exploited to improve the running time of the algorithm. While this optimization is straight forward to implement in the case of sequential code, it has proven to be nontrivial for parallel code even in a homogeneous environment. In this paper, we present a force matrix transformation that is capable of exploiting the symmetries in the force matrix in both a homogeneous and a heterogeneous environment while balancing the load among all the participating processors. The proposed transformation distributes the number of interactions to be computed uniformly among all the slices of the force matrix along any of the axes. The transformed matrix can be scheduled using any well known heterogeneous slice-level scheduling technique. We also derive theoretical bounds for efficiency and load balance for prior work in the literature. We then prove some interesting and useful properties of our transformation and evaluate its advantages and disadvantages. A loop reordering optimization for the symmetric transformation is described. The performance of an MPI implementation of the transformation is studied in terms of the Step Time Variation Ratio (STVR) in a homogeneous and heterogeneous environment.
机译：评估力矩阵构成分子动力学（MD）仿真的最具计算密集的部分。在三体MD模拟中，系统的总能量由系统中的每个独特三次的能量决定，力矩阵是三维的。因此，三体MD算法的执行时间与系统中原子数的立方体成比例。幸运的是，可以利用力矩阵中的对称性来改善算法的运行时间。虽然在顺序代码的情况下，这种优化是直接实现的，但是即使在均匀的环境中，它已经被证明是并行代码的不动性。在本文中，我们介绍了一种力矩阵变换，其能够在均匀和异构环境中利用力矩阵中的对称性，同时平衡所有参与处理器之间的负载。所提出的转换在沿任何轴中的所有轴的所有切片中均匀地分配相互作用的相互作用的数量。可以使用任何众所周知的异构切片级调度技术来调度变换的矩阵。我们还为文献中的事先工作导出了理论界衡的效率和负载余额。然后，我们证明了我们转型的一些有趣和有用的性质，并评估其优缺点。描述了对对称变换的环路重新排序优化。在均匀和异构环境中的步进时间变化比（STVR）方面研究了转换的MPI实现的性能。

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