MISA-MD: A New Design of Molecular Dynamics Software for GPU Architecture.

Molecular dynamics is a significant method in computational material and many other fields, and is computationally intensive. In this paper, we present a new molecular dynamics software, MISA-MD, which is mainly designed for high computational performance on GPU architecture. The main contributions include a redesign of the atom data structure, communication optimizations, parallel strategies and a series of GPU optimizations on memory accessing. Compared to the CPU version, the presented version of MISA-MD can achieve more than 130 speedup when running on GPU hardware. Moreover, our MISAMD code also demonstrates 51 % performance improvement, when compared to the well-known software LAMMPS on GPU.