Computer Science ›› 2018, Vol. 45 ›› Issue (10): 291-294, 299.doi: 10.11896/j.issn.1002-137X.2018.10.054

• Interdiscipline & Frontier • Previous Articles     Next Articles

Cell Verlet Algorithm of Molecular Dynamics Simulation Based on GPU and Its Parallel Performance Analysis

ZHANG Shuai1,2, XU Shun1,3, LIU Qian1,3, JIN Zhong1,3   

  1. Computer Network Information Center,Chinese Academy of Sciences,Beijing 100190,China 1
    University of Chinese Academy of Sciences,Beijing 100049,China 2
    Center of Scientific Computing Applications & Research,Chinese Academy of Sciences,Beijing 100190,China 3
  • Received:2017-12-16 Online:2018-11-05 Published:2018-11-05

Abstract: Molecular dynamics simulation has complexity in spatial and temporal scale,therefore it is critical to optimize the simulation process of molecular dynamics.Based on the characteristics of data parallel on GPU hardware architecture,this paper combined atomic partition and spatial partition of molecular dynamics simulation and optimized the Cell Verlet algorithm for the short-range force calculation,and also designed the core and basic algorithms of molecular dynamics on GPU with optimization and performance analysis.The implementation of Cell Verlet algorithm in this paper is started with atomic partition,each task of particle simulation is mapped to each GPU thread,and then the simulated space is divided into cellular area in the spatial partition way.The cellular index table is established,and the real-time locating simulation particles are realized.Meanwhile,in the force calculation between particles,Hilbert’s space-filling curve algorithm was introduced to keep the partial correlation of particle’s space layout in line with linear data storage,in order to cache and accelerate the access on GPU global memory.This paper also used the memory address alignment and block sharing memory technology to optimize the design of GPU molecular dynamics simulation process.Testing and comparative analysis of examples show that the current implementation of algorithm has advantages in high parallelism and speedup.

Key words: Molecular dynamics, Cell Verlet algorithm, GPU heterogeneous computing, Mutex and synchronization optimization, Locality of memory access

CLC Number: 

  • TP338.6
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