research-article

SW_GROMACS: accelerate GROMACS on Sunway TaihuLight

Authors:

Tingjian Zhang,

Guangwen YangAuthors Info & Claims

SC '19: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

Article No.: 66, Pages 1 - 14

https://doi.org/10.1145/3295500.3356190

Published: 17 November 2019 Publication History

Abstract

GROMACS is one of the most popular Molecular Dynamic (MD) applications and is widely used in the field of chemical and bimolecular system study. Similar to other MD applications, it needs long run-time for large-scale simulations. Therefore, many high performance platforms have been employed to accelerate it, such as Knights Landing (KNL), Cell Processor, Graphics Processing Unit (GPU) and so on. As the third fastest supercomputer in the world, Sunway TaihuLight contains 40960 SW26010 processors and SW26010 is a typical many-core processor. To make full use of the superior computation ability of TaihuLight, we port GROMACS to SW26010 with following new strategies: (1) a new deferred update strategy; (2) a new update mark strategy; (3) a full pipeline acceleration. Furthermore, we redesign GROMACS to enable all possible vectorization. Experiments show that our implementation achieves better performance than both Intel KNL and Nvidia P100 GPU when using appropriate number of SW26010 processors for a fair comparison.

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Cited By

Li XWang ZPan YMeng JFeng SWei Y(2024)Distributed Heterogeneous Spiking Neural Network Simulator Using Sunway AcceleratorsBig Data Mining and Analytics10.26599/BDMA.2024.90200077:4(1301-1320)Online publication date: Dec-2024
https://doi.org/10.26599/BDMA.2024.9020007
Liu ZChu XLv XMeng HLiu HZhu GFu HYang G(2024)SunwayLB: Enabling Extreme-Scale Lattice Boltzmann Method Based Computing Fluid Dynamics Simulations on Advanced Heterogeneous SupercomputersIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2023.334370635:2(324-337)Online publication date: Feb-2024
https://doi.org/10.1109/TPDS.2023.3343706
Lin HYan LChang QLu HLi CHe QSong ZDuan XYin ZLi YLiu ZXue WFu HGan LYang GLiu W(2024)O2ath: an OpenMP offloading toolkit for the sunway heterogeneous manycore platformCCF Transactions on High Performance Computing10.1007/s42514-024-00191-16:3(274-286)Online publication date: 3-May-2024
https://doi.org/10.1007/s42514-024-00191-1
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Index Terms

SW_GROMACS: accelerate GROMACS on Sunway TaihuLight
1. Applied computing
  1. Physical sciences and engineering
    1. Chemistry
2. Computing methodologies
  1. Parallel computing methodologies
    1. Parallel algorithms

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cover image ACM Conferences

SC '19: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

November 2019

1921 pages

ISBN:9781450362290

DOI:10.1145/3295500

General Chair:
Michela Taufer,
Program Chairs:
Pavan Balaji,
Antonio J. Peña

Copyright © 2019 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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SIGHPC: ACM Special Interest Group on High Performance Computing, Special Interest Group on High Performance Computing

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 17 November 2019

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Center for High Performance Computing and System Simulation
Pilot National Laboratory for Marine Science and Technology (Qingdao)
National Key R&D Program of China
National Natural Science Foundation of China

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SC '19

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SIGHPC

SC '19: The International Conference for High Performance Computing, Networking, Storage, and Analysis

November 17 - 19, 2019

Colorado, Denver

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Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

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Cited By

Li XWang ZPan YMeng JFeng SWei Y(2024)Distributed Heterogeneous Spiking Neural Network Simulator Using Sunway AcceleratorsBig Data Mining and Analytics10.26599/BDMA.2024.90200077:4(1301-1320)Online publication date: Dec-2024
https://doi.org/10.26599/BDMA.2024.9020007
Liu ZChu XLv XMeng HLiu HZhu GFu HYang G(2024)SunwayLB: Enabling Extreme-Scale Lattice Boltzmann Method Based Computing Fluid Dynamics Simulations on Advanced Heterogeneous SupercomputersIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2023.334370635:2(324-337)Online publication date: Feb-2024
https://doi.org/10.1109/TPDS.2023.3343706
Lin HYan LChang QLu HLi CHe QSong ZDuan XYin ZLi YLiu ZXue WFu HGan LYang GLiu W(2024)O2ath: an OpenMP offloading toolkit for the sunway heterogeneous manycore platformCCF Transactions on High Performance Computing10.1007/s42514-024-00191-16:3(274-286)Online publication date: 3-May-2024
https://doi.org/10.1007/s42514-024-00191-1
Yu MMa GWang ZTang SChen YWang YLiu YJia DWei Z(2024)swCUDA: Auto parallel code translation framework from CUDA to ATHREAD for new generation sunway supercomputerCCF Transactions on High Performance Computing10.1007/s42514-023-00159-76:4(439-458)Online publication date: 11-Jan-2024
https://doi.org/10.1007/s42514-023-00159-7
Duan XShao QWeng JSchmidt BGan LLi GFu HXue WLiu WYang G(2023)Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight SupercomputerIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2022.322055934:3(881-893)Online publication date: 1-Mar-2023
https://doi.org/10.1109/TPDS.2022.3220559
Qian HWu WZhu QWang FZhao JZheng Y(2023)SWPFOPLD: A Profiling and Optimizing Loader for SW26010Pro Processors2023 8th International Conference on Computer and Communication Systems (ICCCS)10.1109/ICCCS57501.2023.10151092(780-784)Online publication date: 21-Apr-2023
https://doi.org/10.1109/ICCCS57501.2023.10151092
Zhu KLiu CGao YLu JWang DZhang H(2022)Cryo-EM Structure and Activator Screening of Human Tryptophan Hydroxylase 2Frontiers in Pharmacology10.3389/fphar.2022.90743713Online publication date: 15-Aug-2022
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Gao PDuan XSchmidt BZhang WGan LFu HXue WLiu WYang G(2022)Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for InteractionsIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2021.309140833:2(359-373)Online publication date: 1-Feb-2022
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Li YDuan XGan LWan WChen YXu KYang JLiu WXue WFu HYang G(2022)Enabling Large-Scale Simulation of CAM on the Sunway TaihuLight SupercomputerIEEE Transactions on Computers10.1109/TC.2021.306342271:4(824-837)Online publication date: 1-Apr-2022
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Xu JFu JGan LChen YHuang ZYang G(2022)Accelerating cryo-EM Reconstruction of RELION on the New Sunway Supercomputer2022 IEEE Intl Conf on Parallel & Distributed Processing with Applications, Big Data & Cloud Computing, Sustainable Computing & Communications, Social Computing & Networking (ISPA/BDCloud/SocialCom/SustainCom)10.1109/ISPA-BDCloud-SocialCom-SustainCom57177.2022.00024(129-138)Online publication date: Dec-2022
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