Redesigning LAMMPS for Petascale and Hundred-Billion-Atom Simulation on Sunway TaihuLight

Authors: Xiaohui Duan (Shandong University), Ping Gao (Shandong University), Tingjian Zhang (Shandong University), Meng Zhang (Shandong University), Weiguo Liu (Shandong University), Wusheng Zhang (Tsinghua University), Wei Xue (Tsinghua University), Haohuan Fu (Tsinghua University), Lin Gan (Tsinghua University), Dexun Chen (Tsinghua University), Xiangxu Meng (Shandong University), Guangwen Yang (Tsinghua University)

Abstract: Large-scale molecular dynamics (MD) simulations on supercomputers play an increasingly important role in many research areas. In this paper, we present our efforts on redesigning the widely used LAMMPS MD simulator for Sunway TaihuLight supercomputer and its ShenWei many-core architecture (SW26010). The memory constraints of SW26010 bring a number of new challenges for achieving efficient MD implementation on it. In order to overcome these constraints, we employ four levels of optimization: (1) a hybrid memory update strategy; (2) a software cache strategy; (3) customized transcendental math functions; and (4) a full pipeline acceleration. Furthermore, we redesign the code to enable all possible vectorization. Experiments show that our redesigned software on a single SW26010 processor can outperform over 100 E5-2650 cores for running the latest stable release (11Aug17) of LAMMPS. We also achieve a performance of over 2.43 PFlops for a Tersoff simulation when using 16,384 nodes on Sunway TaihuLight.




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