Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST
文献类型：期刊论文
| 作者 | Zhu, You-Liang1; Pan, Deng1; Li, Zhan-Wei1; Liu, Hong2; Qian, Hu-Jun2; Zhao, Yang3; Lu, Zhong-Yuan2; Sun, Zhao-Yan1 |
| 刊名 | MOLECULAR PHYSICS
 |
| 出版日期 | 2018 |
| 卷号 | 116期号:7-8页码:1065-1077 |
| 关键词 | Galamost Molecular Dynamics Multi-gpu Coarse-graining Soft Matter |
| ISSN号 | 0026-8976 |
| DOI | 10.1080/00268976.2018.1434904 |
| 英文摘要 | We describe the algorithm of employing multi-GPU power on the basis of Message Passing Interface (MPI) domain decomposition in a molecular dynamics code, GALAMOST, which is designed for the coarse-grained simulation of soft matters. The code of multi-GPU version is developed based on our previous single-GPU version. In multi-GPU runs, one GPU takes charge of one domain and runs single-GPU code path. The communication between neighbouring domains takes a similar algorithm of CPU-based code of LAMMPS, but is optimised specifically for GPUs. We employ a memory-saving design which can enlarge maximum system size at the same device condition. An optimisation algorithm is employed to prolong the update period of neighbour list. We demonstrate good performance of multi-GPU runs on the simulation of Lennard-Jones liquid, dissipative particle dynamics liquid, polymer and nanoparticle composite, and two-patch particles on workstation. A good scaling of many nodes on cluster for two-patch particles is presented. |
| 语种 | 英语 |
| WOS记录号 | WOS:000430050600025 |
| 出版者 | TAYLOR & FRANCIS LTD |
| 源URL | [http://ir.iccas.ac.cn/handle/121111/45955]  |
| 专题 | 中国科学院化学研究所 |
| 通讯作者 | Lu, Zhong-Yuan |
| 作者单位 | 1.Chinese Acad Sci, Changchun Inst Appl Chem, State Key Lab Polymer Phys & Chem, Changchun, Jilin, Peoples R China 2.Jilin Univ, Inst Theoret Chem, State Key Lab Supramol Struct & Mat, Changchun, Jilin, Peoples R China 3.Natl Supercomp Ctr Tianjin, Tianjin, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhu, You-Liang,Pan, Deng,Li, Zhan-Wei,et al. Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST[J]. MOLECULAR PHYSICS,2018,116(7-8):1065-1077. |
| APA | Zhu, You-Liang.,Pan, Deng.,Li, Zhan-Wei.,Liu, Hong.,Qian, Hu-Jun.,...&Sun, Zhao-Yan.(2018).Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST.MOLECULAR PHYSICS,116(7-8),1065-1077. |
| MLA | Zhu, You-Liang,et al."Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST".MOLECULAR PHYSICS 116.7-8(2018):1065-1077. |
入库方式： OAI收割
来源：化学研究所
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