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Applying high-performance computing in drug discovery and molecular simulation

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National Science Review 2016年第1期3卷 49-63页

作者： Tingting Liu Dong Lu Hao Zhang Mingyue Zheng Huaiyu Yang Yechun Xu Cheng Luo Weiliang Zhu Kunqian Yu Hualiang Jiang State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of Sciences

In recent decades, high-performance computing(HPC) technologies and supercomputers in China have significantly advanced, resulting in remarkable achievements. Computational drug discovery and design,which is based on HPC and combines pharmaceutical chemistry and computational biology, has become a critical approach in drug research and development and is financially supported by the Chinese government. This approach has yielded a series of new algorithms in drug design, as well as new software and databases. This review mainly focuses on the application of HPC to the fields of drug discovery and molecular simulation at the Chinese Academy of Sciences, including virtual drug screening, molecular dynamics simulation, and protein folding. In addition, the potential future application of HPC in precision medicine is briefly discussed.

关键词： high-performance computing computational drug discovery and design virtual screening molecular dynamics simulation protein folding

How Big Data and high-performance computing Drive Brain Science

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Genomics, Proteomics & Bioinformatics 2019年第4期17卷 381-392页

作者： Shanyu Chen Zhipeng He Xinyin Han Xiaoyu He Ruilin Li Haidong Zhu Dan Zhao Chuangchuang Dai Yu Zhang Zhonghua Lu Xuebin Chi Beifang Niu Computer Network Information Center Chinese Academy of Sciences University of Chinese Academy of Sciences Center of Scientific computing Applications&Research Chinese Academy of Sciences Guizhou University School of Medicine

Brain science accelerates the study of intelligence and behavior,contributes fundamental insights into human cognition,and offers prospective treatments for brain *** with the challenges posed by imaging technologies and deep learning computational models,big data and high-performance computing(HPC)play essential roles in studying brain function,brain diseases,and large-scale brain models or *** review the driving forces behind big data and HPC methods applied to brain science,including deep learning,powerful data analysis capabilities,and computational performance solutions,each of which can be used to improve diagnostic accuracy and research *** work reinforces predictions that big data and HPC will continue to improve brain science by making ultrahigh-performance analysis possible,by improving data standardization and sharing,and by providing new neuromorphic insights.

关键词： Brain science Big data high-performance computing Brain connectomes Deep learning

New prospects for computational hydraulics by leveraging high-performance heterogeneous computing techniques

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Journal of Hydrodynamics 2016年第6期28卷 977-985页

作者： Qiuhua LIANG Luke SMITH Xilin XIA Hebei University of Engineering Handan 056038 China School of Civil Engineering and Geosciences Newcastle University Newcastle upon Tyne UK

In the last two decades, computational hydraulics has undergone a rapid development following the advancement of data acquisition and computing technologies. Using a finite-volume Godunov-type hydrodynamic model, this work demonstrates the promise of modern high-performance computing technology to achieve real-time flood modeling at a regional scale. The software is implemented for high-performance heterogeneous computing using the OpenCL programming framework, and developed to support simulations across multiple GPUs using a domain decomposition technique and across multiple systems through an efficient implementation of the Message Passing Interface （MPI） standard. The software is applied for a convective storm induced flood event in Newcastle upon Tyne, demonstrating high computational performance across a GPU cluster, and good agreement against crowd- sourced observations. Issues relating to data availability, complex urban topography and differences in drainage capacity affect results for a small number of areas.

关键词： computational hydraulics high-performance computing flood modeling shallow water equations shock-capttLring hydrodynamic model

Optimization Techniques for GPU-Based Parallel Programming Models in high-performance computing

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信息工程期刊（中英文版） 2024年第1期12卷 7-11页

作者： Shuntao Tang Wei Chen Xihua University

This study embarks on a comprehensive examination of optimization techniques within GPU-based parallel programming models,pivotal for advancing high-performance computing(HPC).Emphasizing the transition of GPUs from graphic-centric processors to versatile computing units,it delves into the nuanced optimization of memory access,thread management,algorithmic design,and data *** optimizations are critical for exploiting the parallel processing capabilities of GPUs,addressingboth the theoretical frameworks and practical *** integrating advanced strategies such as memory coalescing,dynamic scheduling,and parallel algorithmic transformations,this research aims to significantly elevate computational efficiency and *** findings underscore the potential of optimized GPU programming to revolutionize computational tasks across various domains,highlighting a pathway towards achieving unparalleled processing power and efficiency in HPC *** paper not only contributes to the academic discourse on GPU optimization but also provides actionable insights for developers,fostering advancements in computational sciences and technology.

关键词： Optimization Techniques GPU-Based Parallel Programming Models high-performance computing

Software approaches for resilience of high performance computing systems:a survey

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Frontiers of Computer Science 2023年第4期17卷 43-56页

作者： Jie JIA Yi LIU Guozhen ZHANG Yulin GAO Depei QIAN School of Computer Science and Engineering Beihang UniversityBeijing 100191China Sino-German Joint Software Institute Beihang UniversityBeijing 100191China

With the scaling up of high-performance computing systems in recent years,their reliability has been descending ***,system resilience has been regarded as one of the critical challenges for large-scale HPC *** techniques and systems have been proposed to ensure the correct execution and completion of parallel *** paper provides a comprehensive survey of existing software resilience ***,a classification of software resilience approaches is presented;then we introduce major approaches and techniques,including checkpointing,replication,soft error resilience,algorithmbased fault tolerance,fault detection and *** addition,challenges exposed by system-scale and heterogeneous architecture are also discussed.

关键词： resilience high-performance computing fault tolerance challenge

Mobile Multimedia computing in Cyber-Physical Surveillance Services Through UAV-Borne Video-SAR:A Taxonomy of Intelligent Data Processing for IoMT-Enabled Radar Sensor Networks

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Tsinghua Science and Technology 2022年第2期27卷 288-302页

作者： Mohammad R.Khosravi Sadegh Samadi Department of Electrical and Electronics Engineering Shiraz University of TechnologyShiraz 313-71555Iran

This study investigates the different aspects of multimedia computing in Video Synthetic Aperture Radar(Video-SAR)as a new mode of radar imaging for real-time remote sensing and *** research also considers new suggestions in the systematic design,research taxonomy,and future trends of radar data *** the conventional modes of SAR imaging,Video-SAR can generate video sequences to obtain online monitoring and green surveillance throughout the day and night(regardless of light sources)in all ***,an introduction to Video-SAR is ***,some specific properties of this imaging mode are ***,this research covers one of the most important aspects of the Video-SAR systems,namely,the systematic design requirements,and also some new types of visual distortions which are different from the distortions,artifacts and noises observed in the conventional imaging *** addition,some topics on the general features and high-performance computing of Video-SAR towards radar communications through Unmanned Aerial Vehicle(UAV)platforms,Internet of Multimedia Things(IoMT),Video-SAR data processing issues,and real-world applications are investigated.

关键词： Video Synthetic Aperture Radar(Video-SAR)imaging radar networks radar image processing high-performance computing Internet of Multimedia Things(IoMT) cybersecurity

Spatial cloud computing: how can the geospatial sciences use and help shape cloud computing?

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International Journal of Digital Earth 2011年第4期4卷 305-329页

作者： Chaowei Yang Michael Goodchild Qunying Huang Doug Nebert Robert Raskin Yan Xu Myra Bambacus Daniel Fay Department of Geography and GeoInformation Science and Center for Intelligent Spatial computing George Mason UniversityFairfax VA 22030-4444USA Department of Geography University of California5707 Ellison HallSanta Barbara CA 93106-4060USA Federal Geographic Data Committee 590 National CenterReston VA 20192USA NASA Jet Propulsion Laboratory 4800 Oak Grove Drive PasadenaCA 91109USA Microsoft Research Connections MicrosoftRedmondWAUSA NASA Goddard Space Flight Center Code 700GreenbeltMD 20771USA

The geospatial sciences face grand information technology(IT)challenges in the twenty-first century:data intensity,computing intensity,concurrent access intensity and spatiotemporal *** challenges require the readiness of a computing infrastructure that can:(1)better support discovery,access and utilization of data and data processing so as to relieve scientists and engineers of IT tasks and focus on scientific discoveries;(2)provide real-time IT resources to enable real-time applications,such as emergency response;(3)deal with access spikes;and(4)provide more reliable and scalable service for massive numbers of concurrent users to advance public *** emergence of cloud computing provides a potential solution with an elastic,on-demand computing platform to integrateobservation systems,parameter extracting algorithms,phenomena simulations,analytical visualization and decision support,and to provide social impact and user feedbackthe essential elements of the geospatial *** discuss the utilization of cloud computing to support the intensities of geospatial sciences by reporting from our investigations on how cloud computing could enable the geospatial sciences and how spatiotemporal principles,the kernel of the geospatial sciences,could be utilized to ensure the benefits of cloud *** research examples are presented to analyze how to:(1)search,access and utilize geospatial data;(2)configure computing infrastructure to enable the computability of intensive simulation models;(3)disseminate and utilize research results for massive numbers of concurrent users;and(4)adopt spatiotemporal principles to support spatiotemporal intensive *** paper concludes with a discussion of opportunities and challenges for spatial cloud computing(SCC).

关键词： digital earth Cyber GIS geodynamics space-time high-performance computing geospatial cyberinfrastructure

A geospatial hybrid cloud platform based on multi-sourced computing and model resources for geosciences

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International Journal of Digital Earth 2018年第12期11卷 1184-1204页

作者： Qunying Huang Jing Li Zhenlong Li Department of Geography University of Wisconsin–MadisonMadisonWIUSA Department of Geography and the Environment University of DenverDenverCOUSA Department of Geography University of South CarolinaColumbiaSCUSA

Cloud computing has been considered as the next-generation computing platform with the potential to address the data and computing challenges in ***,only a limited number of geoscientists have been adapting this platform for their scientific research mainly due to two barriers:1)selecting an appropriate cloud platform for a specific application could be challenging,as various cloud services are available and 2)existing general cloud platforms are not designed to support geoscience applications,algorithms and *** tackle such barriers,this research aims to design a hybrid cloud computing(HCC)platform that can utilize and integrate the computing resources across different organizations to build a unified geospatial cloud computing *** platform can manage different types of underlying cloud infrastructure(e.g.,private or public clouds),and enables geoscientists to test and leverage the cloud capabilities through a web ***,the platform also provides different geospatial cloud services,such as workflow as a service,on the top of common cloud services(e.g.,infrastructure as a service)provided by general cloud ***,geoscientists can easily create a model workflow by recruiting the needed models for a geospatial application or task on the fly.A HCC prototype is developed and dust storm simulation is used to demonstrate the capability and feasibility of such platform in facilitating geosciences by leveraging across-organization computing and model resources.

关键词： Cloud computing Big Data geospatial cloud services workflow as a service(WaaS) geoprocessing as a service(GaaS) model as a service(MaaS) high-performance computing parallel computing

Parallel optimization of underwater acoustic models:A survey

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Chinese Physics B 2022年第10期31卷 189-207页

作者： Zi-jie Zhu Shu-qing Ma Xiao-Qian Zhu Qiang Lan Sheng-Chun Piao Yu-Sheng Cheng College of Computer Science and Technology National University of Defense TechnologyChangsha 410073China College of Meteorology and Oceanography National University of Defense TechnologyChangsha 410073China Acoustic Science and Technology Laboratory Harbin Engineering UniversityHarbin 150001China Underwater Acoustics Center Navy Submarine AcademyQingdao 266000China

Underwater acoustic models are effective tools for simulating underwater sound *** than 50 years of research have been conducted on the theory and computational models of sound propagation in the ***,underwater sound propagation models were unable to solve practical large-scale three-dimensional problems for many years due to limited computing power and hardware *** the mid-1980s,research on high performance computing for acoustic propagation models in the field of underwater acoustics has flourished with the emergence of high-performance computing platforms,enabling underwater acoustic propagation models to solve many practical application problems that could not be solved *** this paper,the contributions of research on high-performance computing for underwater acoustic propagation models since the 1980s are thoroughly reviewed and the possible development directions for the future are outlined.

关键词： underwater acoustic models underwater sound propagation high-performance computing modeling three-dimensional problems