标题:A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer
作者:Peng, Shaoliang; Cui, Yingbo; Yang, Shunyun; Su, Wenhe; Zhang, Xiaoyu; Zhang, Tenglilang; Liu, Weiguo; Zhao, Xing-Ming
通讯作者:Peng, Shaoliang;Peng, SL;Peng, SL
作者机构:[Peng, Shaoliang] Hunan Univ, Natl Supercomp Ctr, Changsha Coll Informat Sci & Engn, Changsha 410006, Hunan, Peoples R China.; [Peng, Shaoliang; Cui 更多
会议名称:27th International Conference on Genome Informatics (GIW)
会议日期:OCT 03-05, 2016
来源:IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
出版年:2019
卷:16
期:2
页码:425-433
DOI:10.1109/TCBB.2017.2713362
关键词:GROMACS; molecular dynamics simulation; high performance computing;; parallel framework
摘要:Molecular Dynamics (MD) is the simulation of the dynamic behavior of atoms and molecules. As the most popular software for molecular dynamics, GROMACS cannot work on large-scale data because of limit computing resources. In this paper, we propose a CPU and Intel (R) Xeon Phi Many Integrated Core (MIC) collaborated parallel framework to accelerate GROMACS using the offload mode on a MIC coprocessor, with which the performance of GROMACS is improved significantly, especially with the utility of Tianhe-2 supercomputer. Furthermore, we optimize GROMACS so that it can run on both the CPU and MIC at the same time. In addition, we accelerate multi-node GROMACS so that it can be used in practice. Benchmarking on real data, our accelerated GROMACS performs very well and reduces computation time significantly. Source code: https://github.com/tianhe2/gromacs-mic.
收录类别:CPCI-S;EI;SCIE
WOS核心被引频次:2
资源类型:会议论文;期刊论文
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