| GROMACS软件并行计算性能分析 |
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| 引用本文： | 张宝花,徐顺.GROMACS软件并行计算性能分析[J].计算机系统应用,2016,25(12):16-23. |
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| 作者姓名： | 张宝花 徐顺 |
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| 作者单位： | 中国科学院计算机网络信息中心 超级计算中心, 北京 100190,中国科学院计算机网络信息中心 超级计算中心, 北京 100190 |
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| 基金项目： | 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） |
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| 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+OpenMP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、OpenMP、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.
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| 关 键 词： | 分子动力学模拟 GROMACS 并行计算 |
| 收稿时间： | 2016/3/24 0:00:00 |
| 修稿时间： | 2016/4/27 0:00:00 |
Parallel Computing Performance Analysis on GROMACS Software |
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| ZHANG Bao-Hua and XU Shun.Parallel Computing Performance Analysis on GROMACS Software[J].Computer Systems& Applications,2016,25(12):16-23. |
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| Authors: | ZHANG Bao-Hua and XU Shun |
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| Affiliation: | Supercomputing Center, Computer Network Information Center, CAS, Beijing 100190, China and Supercomputing Center, Computer Network Information Center, CAS, Beijing 100190, China |
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| Abstract: | 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 OpenMP 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/OpenMP and GPU to obtain the best performance. |
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| Keywords: | molecule dynamic simulation GROMACS parallel computing |
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