Memory Access Optimization of Molecular Dynamics Simulation Software Crystal-MD on Sunway TaihuLight

JJ Li and J Lin and PP Du and K Zhang and J Wu, TSINGHUA SCIENCE AND TECHNOLOGY, 26, 296-308 (2021).

DOI: 10.26599/TST.2019.9010074

The radiation damage effect of key structural materials is one of the main research subjects of the numerical reactor. From the perspective of experimental safety and feasibility, Molecular Dynamics (MD) in the materials field is an ideal method for simulating the radiation damage of structural materials. The Crystal-MD represents a massive parallel MD simulation software based on the key material characteristics of reactors. Compared with the Large-scale Atomic/Molecurlar Massively Parallel Simulator (LAMMPS) and ITAP Molecular Dynamics (IMD) software, the Crystal-MD reduces the memory required for software operation to a certain extent, but it is very time-consuming. Moreover, the calculation results of the Crystal-MD have large deviations, and there are also some problems, such as memory limitation and frequent communication during its migration and optimization. In this paper, in order to solve the above problems, the memory access mode of the Crystal-MD software is studied. Based on the memory access mode, a memory access optimization strategy is proposed for a unique architecture of China's supercomputer Sunway TaihuLight. The proposed optimization strategy is verified by the experiments, and experimental results show that the running speed of the Crystal-MD is increased significantly by using the proposed optimization strategy.

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