MPI+OpenMP混合并行编程模型在分子动力学中的应用  

Application of MPI+OpenMP hybrid parallel programming model in molecular dynamics

作　　者：张坤峰 张苏 ZHANG Kunfeng;ZHANG Su(School of Computer Science and Technology,Zhoukou Normal University,Zhoukou 466001)

机构地区：[1]周口师范学院计算机科学与技术学院,河南周口466001

出　　处：《周口师范学院学报》2022年第5期71-75,共5页Journal of Zhoukou Normal University

摘　　要：针对分子动力学串行计算速度不足问题,设计一种基于MPI+OpenMP的并行编程模型,实现LAMMPS并行计算。从而满足在节点间采用MPI进行消息传递并行,在节点内采用OpenMP共享内存模式多线程并行;最后根据分子动力学自身计算特点,对近邻表的构建以及力的计算进行优化,同时将并行结果和串行结果以及纯OpenMP运行时间和混合模型运行时间作对比。实验结果表明,采用MPI+OpenMP混合并行编程模型不仅能够加快计算速度,而且具有很好的扩展性。A parallel programming model based on MPI+OpenMP was proposed to realize LAMMPS multi-layer parallelism.Therefore,MPI is used for message passing parallelism among nodes and OpenMP shared memory is used for multi-thread parallelism within nodes.According to the computational characteristics of molecular dynamics,the construction of the nearest neighbor table and the calculation of the force were optimized,and the parallel results and serial results as well as the running time of pure OpenMP and hybrid model were compared.The experimental results show that the MPI+OpenMP hybrid parallel programming model can not only accelerate the computational speed,but also has good scalability.

关 键 词：分子动力学 MPI+OPENMP 并行编程模型 LAMMPS 

分 类 号：TP39[自动化与计算机技术—计算机应用技术]