swMD: Performance Optimizations for Molecular Dynamics Simulation on Sunway Taihulight
Kun Li, Shigang Li, Bei Wang, Yifeng Chen, Yunquan Zhang · 2019
Molecular dynamics is an extensively utilized computational tool for solids, liquids and molecules simulation. Currently, much research on molecular dynamics simulation focuses on simplifying forces or parallelizing tasks to reduce the overheads of forces computation. However, the molecular dynamics simulation still remains challenging since the communication and neighbor list construction are time-consuming in the existing algorithm. In this paper, we propose a swMD optimization strategy including a new communication mode called ghost communication to reduce superfluous communication overheads and an innovative neighbor list algorithm to improve the construction efficiency of it. Moreover, we accelerate computation by utilizing many-core resources on Sunway Taihulight and present an auto-tuning Producer-Consumer pairing algorithm to make neighbor list construction happen in fast register communication. Compared to traditional methods, swMD optimization strategy obtains a maximal 82.2% and an average of 79.4% performance improvement. We also evaluate the scalability up to 266,240 cores and the results demonstrate the high efficiency of swMD optimization strategy on communication, computation and neighbor list construction respectively.