MD3DOCKxb: An ultra-scalable CPU-MIC coordinated virtual screening framework
文献类型：会议论文
| 作者 | Peng, Shaoliang2; Zhang, Xiaoyu2; Yang, Shunyun2; Su, Wenhe2; Zhang, Zhiqiang2; Dong, Dong2; Lu, Kai3; Lu, Yutong2; Liao, Xiangke2; Schmidt, Bertil4 |
| 出版日期 | 2017-07-10 |
| DOI | 10.1109/CCGRID.2017.131 |
| 页码 | 671-676 |
| 英文摘要 | Molecular docking is an important method in computational drug discovery. In large-scale virtual screening, millions of small drug-like molecules (chemical compounds) are compared against a designated target protein (receptor). Depending on the utilized docking algorithm for screening, this can take several weeks on conventional HPC systems. However, for certain applications including large-scale screening tasks for newly emerging infectious diseases such high runtimes can be highly prohibitive. In this paper, we investigate how the massively parallel neo-heterogeneous architecture of Tianhe-2 Supercomputer consisting of thousands of nodes comprising CPUs and MIC coprocessors that can efficiently be used for virtual screening tasks. Our proposed approach is based on a coordinated parallel framework called mD3DOCKxb in which CPUs collaborate with MICs to achieve high hardware utilization. mD3DOCKxb comprises a novel efficient communication engine for dynamic task scheduling and load balancing between nodes in order to reduce communication and I/O latency. This results in a highly scalable implementation with parallel efficiency of over 84% (strong scaling) when executing on 8,000 Tianhe-2 nodes comprising 192,000 CPU cores and 1,368,000 MIC cores. |
| 会议录 | Proceedings - 2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, CCGRID 2017
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| 会议录出版者 | Institute of Electrical and Electronics Engineers Inc. |
| 文献子类 | Proceedings Paper |
| 语种 | 英语 |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/266849]  |
| 专题 | 药物发现与设计中心 |
| 通讯作者 | Peng, Shaoliang |
| 作者单位 | 1.Department of Computer Science and Information Engineering, Providence University, Taiwan 2.School of Computer Science, National University of Defense Technology, Changsha, China; 3.National Supercomputing Center in Guangzhou, Sun Yat-sen University, Guangzhou, China; 4.Institute of Computer Science, Johannes Gutenberg University, Mainz, Germany; 5.State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; |
| 推荐引用方式 GB/T 7714 | Peng, Shaoliang,Zhang, Xiaoyu,Yang, Shunyun,et al. MD3DOCKxb: An ultra-scalable CPU-MIC coordinated virtual screening framework[C]. 见:. |
入库方式： OAI收割
来源：上海药物研究所
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