摘要
分子动力学模拟是对微观分子原子体系在时间与空间上的运动模拟,是从微观本质上认识体系宏观性质的有力方法.针对如何提升分子动力学并行模拟性能的问题,本文以著名软件GROMACS为例,分析其在分子动力学模拟并行计算方面的实现策略,结合分子动力学模拟关键原理与测试实例,提出MPI+Open MP并行环境下计算性能的优化策略,为并行计算环境下实现分子动力学模拟的最优化计算性能提供理论和实践参考.对GPU异构并行环境下如何进行MPI、Open MP、GPU搭配选择以达到性能最优,本文亦给出了一定的理论和实例参考.
Molecule dynamic（MD） simulation is used for simulation of atomic systems. It is a powerful tool for understanding relationships between microcosmic nature and macroscopic properties. In view of the problem of how to improve the performance of parallel MD simulations, in this paper taking the famous GROMACS software as an example, we study its implementation strategy on parallel computing performance, combining with the key principles of MD and the results of test cases, and we propose optimization strategies of performance under MPI and Open MP parallel environment. It can provide theoretical and practical reference for optimizing performance of MD software. In addition, we also study that in the GPU heterogeneous parallel environment how to tune MPI/Open MP and GPU to obtain the best performance.
出处
《计算机系统应用》
2016年第12期16-23,共8页
Computer Systems & Applications
基金
中国科学院青年创新促进会(2016156)
"一三五"规划重点培育方向专项项目(CNIC_PY_1404)
