摘要
【目的】异构计算已经成为高性能计算的重要组成部分,GPU异构计算可显著提速计算密集型的分子动力学模拟应用,本文介绍自研分子动力学模拟软件eMD的系统设计及其异构计算应用。【方法】首先介绍eMD软件的目标定位,包括应用功能和计算性能两方面;然后介绍软件概要设计,包括框架、模块和接口等组成部分;重点围绕面向异构计算的软件架构设计和移植优化技术进行阐述。【结果】eMD软件系统基于GPU异构计算可实现大规模体系模拟,同时提供特色的分子动力学模拟算法和模型。【结论】eMD将充分发挥GPU异构计算算力,以提升分子动力学模拟应用效率,助力分子建模理论方法的创新应用和分子科学问题的研究。
[Objective]Heterogeneous computing has become an important part of high-performance computing.GPU heterogeneous computing can significantly accelerate computationally intensive molecular dynamics simulation applications.This paper introduces the system design of a selfdeveloped molecular dynamics simulation software eMD and its application on heterogeneous computing systems.[Methods]This paper first introduces the design objectives of the eMD software including application functionality and computing performance;presents the outline of software design including the framework,modules and interfaces;and then focuses on the software architecture design and porting optimization technology for heterogeneous computing.[Results]The eMD software system can achieve large-scale system simulation based on GPU heterogeneous computing while providing unique molecular dynamics simulation algorithms and models.[Conclusions]eMD will fully leverage the heterogeneous computing power of GPU to improve the efficiency of molecular dynamics simulation applications,and to assist in innovative application of molecular modeling theory and methods and research of molecular science problems.
作者
徐顺
张宝花
刘倩
金钟
XU Shun;ZHANG Baohua;LIU Qian;JIN Zhong(Computer Network Information Center,Chinese Academy of Sciences,Beijing 100083,China)
出处
《数据与计算发展前沿》
CSCD
2024年第1期21-34,共14页
Frontiers of Data & Computing
基金
国家重点研发计划课题“多物理复杂体系科学计算应用平台”(2020YFB0204802)
甘肃省科技计划项目“甘肃省生物医药高性能计算示范平台”(21YF5GA005)。
关键词
分子动力学
GPU异构计算
并行计算
国产超算
molecular dynamics
GPU heterogeneous computing
parallel computing
domestic supercomputer
