Implementing Molecular Dynamics Simulation on Sunway TaihuLight System
WQ Dong and LT Kang and Z Quan and KL Li and KQ Li and ZY Hao and XH Xie, PROCEEDINGS OF 2016 IEEE 18TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING AND COMMUNICATIONS; IEEE 14TH INTERNATIONAL CONFERENCE ON SMART CITY; IEEE 2ND INTERNATIONAL CONFERENCE ON DATA SCIENCE AND SYSTEMS (HPCC/SMARTCITY/DSS), 443-450 (2016).
Molecular dynamics (MD) simulation is a common tool to study the physical movements of atoms and molecules in many research fields. However, it is an extremely time-consuming application which takes researchers weeks or months to run a single simulation when simulation size scales up and computing demands keep growing. In this paper, an improved MD implementation on Sunway TaihuLight supercomputer is developed to solve the above mentioned issues. The new implementation is extended from an existing implementation (i. e., LAMMPS) which widely uses the MD application. Sunway TaihuLight is a heterogeneous supercomputer with a fully customized integration approach and a brand new many-core processor SW26010. The Sunway TaihuLight takes the world's first place with peak performance over 100PFlops. We propose an optimization method of the MD simulation in three steps: paralleled extensions to SW26010, memory-access optimizations, and vectorization. After the optimization process, an 8x speedup is achieved on a single computing node. Superiorly, we also scale up to 95 thousands computing nodes (6 millions cores) with an almost leaner speedup. Besides, the proposed methods can also be applied to many other molecular dynamics codes, or similar applications.
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