A Communication-Avoiding Algorithm for Molecular Dynamics Simulation
文献类型：会议论文
| 作者 | Wang, Bei1; Chen, Yifeng1; Hou, Chaofeng2 |
| 出版日期 | 1905-07-12 |
| 会议日期 | December 9, 2019 - December 11, 2019 |
| 会议地点 | Melbourne, VIC, Australia |
| 关键词 | Supercomputers - Bandwidth - Iterative methods - Electronic data interchange |
| 卷号 | 11944 LNCS |
| DOI | 10.1007/978-3-030-38991-8_6 |
| 页码 | 75-88 |
| 英文摘要 | Molecular dynamics and many similar time-dependent computing tasks are defined as simple state updates over multiple time steps. In recent years, modern supercomputing clusters have enjoyed fast-growing compute capability and moderate-growing memory bandwidth, but their improvement of network bandwidth/latency is limited. In this paper, we propose a new communication-avoiding algorithmic model based on asynchronous communications which, unlike BSP, records and handles multiple iterative states together. The basic idea is to let computation run in small regular time steps while communications over longer dynamic time steps. Computation keeps checking inaccuracies so that the intervals between communications are small in volatile scenarios but longer when dynamics is smooth. This helps reduce the number of data exchanges via network communication and hence improve the overall performance when communication is the bottleneck. We test MD simulation of condensed covalent materials on the Sunway TaihuLight. For best time-to-solution, the general-purpose supercomputer Sunway TaihuLight performs 11.8聽K steps/s for a system with 2.1 million silicon atoms and 5.1聽K steps/s for 50.4 million silicon atoms. This time-to-solution performance is close to those of state-of-art hardware solution. A software solution using general-purpose supercomputers makes the technology more accessible to the general scientific users. 漏 2020, Springer Nature Switzerland AG. |
| 项目编号 | Supported by National 2017YFB0202000. |
| 资助机构 | Springer Science and Business Media Deutschland GmbH |
| 会议录 | 19th International Conference on Algorithms andArchitectures for Parallel Processing, ICA3PP 2019
 |
| 学科主题 | Molecular Dynamics |
| 源URL | [http://ir.ipe.ac.cn/handle/122111/59248]  |
| 作者单位 | 1.EECS, Peking University, Beijing; 100871, China 2.Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China |
| 推荐引用方式 GB/T 7714 | Wang, Bei,Chen, Yifeng,Hou, Chaofeng. A Communication-Avoiding Algorithm for Molecular Dynamics Simulation[C]. 见:. Melbourne, VIC, Australia. December 9, 2019 - December 11, 2019. |
入库方式： OAI收割
来源：过程工程研究所
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