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Extraction of drainage networks from large terrain datasets using high throughput computing

COMPUTERS & GEOSCIENCES 2009年第2期35卷 337-346页

作者： Gong, Jianya Xie, Jibo Wuhan Univ State Key Lab Informat Engn Surveying Mapping & R Wuhan 430079 Peoples R China

Advanced digital photogrammetry and remote sensing technology produces large terrain datasets (LTD). How to process and use these LTD has become-a big challenge for GIS users. Extracting drainage networks, which are basic for hydrological applications, from LTD is one of the typical applications of digital terrain analysis (DTA) in geographical information applications. Existing serial drainage algorithms cannot deal with large data volumes in a timely fashion, and few GIS platforms can process LTD beyond the GB size. High throughput computing (HTC) a distributed parallel computing mode, is proposed to improve the efficiency of drainage networks extraction from LTD. Drainage network extraction using HTC involves two key issues: (1) how to decompose the large DEM datasets into independent computing units and (2) how to merge the separate outputs into a final result. A new decomposition method is presented in which the large datasets are partitioned into independent computing units using natural watershed boundaries instead of using regular 1-dimensional (strip-wise) and 2-dimensional (block-wise) decomposition. Because the distribution of drainage networks is strongly related to watershed boundaries, the new decomposition method is more effective and natural. The method to extract natural watershed boundaries was improved by using multi-scale DEMs instead of single-scale DEMs. A HTC environment is employed to test the proposed methods with real datasets. (c) 2008 Elsevier Ltd. All rights reserved.

关键词： Digital terrain analysis Extraction of drainage networks distributed parallel computing High throughput computing Multi-scale decomposition

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Industrial scale Large Eddy Simulations with adaptive octree meshes using immersogeometric analysis

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COMPUTERS & MATHEMATICS WITH APPLICATIONS 2021年 97卷 28-44页

作者： Saurabh, Kumar Gao, Boshun Fernando, Milinda Xu, Songzhe Khanwale, Makrand A. Khara, Biswajit Hsu, Ming-Chen Krishnamurthy, Adarsh Sundar, Hari Ganapathysubramanian, Baskar Iowa State Univ Dept Mech Engn Ames IA 50010 USA Iowa State Univ Dept Math Ames IA 50010 USA Univ Utah Sch Comp Salt Lake City UT 84112 USA

We present a variant of the immersed boundary method integrated with octree meshes for highly efficient and accurate Large Eddy Simulations (LES) of flows around complex geometries. We demonstrate the scalability of the proposed method up to theta(32K) processors. This is achieved by (a) rapid in-out tests;(b) adaptive quadrature for an accurate evaluation of forces;(c) tensorized evaluation during matrix assembly. We showcase this method on two non-trivial applications: accurately computing the drag coefficient of a sphere across Reynolds numbers 1 - 10(6) encompassing the drag crisis regime;simulating flow features across a semi-truck for investigating the effect of platooning on efficiency.

关键词： Weak boundary conditions Immersogeometric analysis Octrees Continuous Galerkin method Drag crisis distributed parallel computing

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BUILDING A VIRTUAL MACHINE-ROOM - A FOCAL POINT IN METAcomputing

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FUTURE GENERATION COMPUTER SYSTEMS 1995年第4-5期11卷 477-489页

作者： RAMME, F Paderbom Center for Parallel Computing University of Paderborn Warburger Str. 100 33095 Paderbom Germany

computing resources which are transparently available to the user via networked environments are commonly called a metacomputer. In this sense, a metacomputer is a network of heterogeneous, computational resources linked by software in such a way that they can be used as easily as a single computational unit. During the last few years our work has been concentrated on developing methods and tools to provide a transparent and vendor independent hardware management system to the users. Solving this problem up to a high abstraction level will bring the idea of metacomputing a large step closer to its fruition. After reviewing the metacomputing approaches in Europe and the States, we will break down the task force into almost independent units. One of these, the resource access and allocation problem, the project computing Center Software was focused on. This paper takes a closer look at CCS. Its underlying model which uses abstract views for specifying system components and the general purpose Resource Description Language will be sketched. We will explain how it is possible to support Wide-Area Network access and unstable connection lines. Afterwards, we will present the system and vendor independent batch processing facility usable for arbitrary programming environments. On-going activities and an enhancement of the CCS methodology to solve a core problem in wide-area metacomputing will conclude this paper.

关键词： distributed parallel computing RESOURCE AND ACCESS MANAGEMENT METAcomputing HETEROGENEOUS SYSTEM INTEGRATION

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***: an online NGS data interpretation system based on intelligent gene ranking and large-scale text mining

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BMC MEDICAL GENOMICS 2019年第1期12卷 1-10页

作者： Jiang, Yanhuang Wu, Chengkun Zhang, Yanghui Zhang, Shaowei Yu, Shuojun Lei, Peng Lu, Qin Xi, Yanwei Wang, Hua Song, Zhuo Genetalks Biotech Co Ltd Changsha 410000 Peoples R China Natl Univ Def Technol Coll Comp State Key Lab High Performance Comp Changsha 410073 Peoples R China Hunan Prov Maternal & Child Hlth Care Hosp NHC Key Lab Birth Defects Res Prevent & Treatment 53 Xiangchun Rd Changsha 410008 Peoples R China Royal Univ Hosp Cytogenet & Human Mol Genet Labs Saskatoon SK Canada Hunan Prov Maternal & Child Hlth Care Hosp Changsha 410073 Peoples R China

Background: An important task in the interpretation of sequencing data is to highlight pathogenic genes (or detrimental variants) in the field of Mendelian diseases. It is still challenging despite the recent rapid development of genomics and bioinformatics. A typical interpretation workflow includes annotation, filtration, manual inspection and literature review. Those steps are time-consuming and error-prone in the absence of systematic support. Therefore, we developed ***, an online DNA sequencing interpretation system, which prioritizes genes and variants for novel disease-gene relation discovery and integrates text mining results to provide literature evidence for the discovery. Its phenotype-driven ranking and biological data mining approach significantly speed up the whole interpretation process. Results: The *** system is freely available as a web portal at http://*** for academic research. Evaluation on the DDD project dataset demonstrates an accuracy of 77% (235 out of 305 cases) for top-50 genes and an accuracy of 41.6% (127 out of 305 cases) for top-5 genes. Conclusions: *** provides an intelligent web portal for genomics data interpretation via the integration of bioinformatics tools, distributed parallel computing, biomedical text mining. It can facilitate the application of genomic analytics in clinical research and practices.

关键词： NGS data interpretation Gene prioritization Neural network Text mining distributed parallel computing

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Visualization and management of large-scale data on SX-6

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NEC RESEARCH & DEVELOPMENT 2003年第1期44卷 95-98页

作者： Kameyama, T Nakano, E Takei, T Yoshida, A Takahara, H NEC Corp Ltd HPC Mkt Promot Div Tokyo Japan NEC Corp Ltd Internet Syst Res Labs Tokyo Japan

There have been ever-increasing requirements for the efficient storage, management, and visualization of large volumes of data resulting from high performance computing with the increased computing capabilities of sup... 详细信息

关键词： visualization large-scale data data storage hierarchical data database system distributed parallel computing RVSLIB web computing supercomputing

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A parallel computing strategy for Monte Carlo simulation using groundwater models

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GEOFISICA INTERNACIONAL 2015年第3期54卷 245-254页

作者： Leyva-Suarez, Esther Herrera, Graciela S. de la Cruz, Luis M. Univ Nacl Autonoma Mexico Posgrad Ciencias Tierra Mexico City 04510 DF Mexico Univ Nacl Autonoma Mexico Inst Geofis Mexico City 04510 DF Mexico

In this paper we present the results of a parallelization strategy to reduce the execution time for applying Monte Carlo simulation with a large number of realizations obtained using a groundwater flow and transport model. We develop a script in Python using mpi4py, in order to execute GWMC and related programs in parallel, applying the MPI library. Our approach is to calculate the initial inputs for each realization, and run groups of these realizations in separate processors and afterwards to calculate the mean vector and the covariance matrix of them. This strategy was applied to the study of a simplified aquifer in a rectangular domain of a single layer. We report the results of speedup and efficiency for 1000, 2000 and 4000 realizations for different number of processors. Efficiencies of 0.70, 0.76 and 0.75 were obtained for 64, 64 and 96 processors, respectively. We observe a slightly improvement of the performance as the number of realizations is increased.

关键词： groundwater flow and transport Monte Carlo simulation distributed parallel computing Python

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A Two-Level Cross-Sectional Optimization Approach for Automotive Body Concept Design

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Automotive Innovation 2018年第2期1卷 122-130页

作者： Huan Qin Zijian Liu Yu Liu Haolong Zhong State Key Laboratory of Advanced Design and Manufacturing for Vehicle Body Hunan UniversityChangsha 410082China College of Mechanical and Vehicle Engineering Hunan UniversityChangsha 410082China

Concept design is vital important in development of auto-body and it has great effects on later design *** this paper,a twolevel cross-sectional optimization approach is presented to shorten concept design ***,an exact structural analysis approach for spatial semi-rigid framed structures,i.e.,the transfer stiffness matrix method proposed in our previous study,is adopted for both static and dynamic analyses of body-in-white(BIW)structure.A two-level cross-sectional optimization approach is then proposed for an automotive BIW lightweight design,and genetic algorithm is used to solve the optimization ***,an object-oriented MATLAB toolbox,using distributed parallel computing techniques,is developed to promote the concept design of the BIW ***,relevant numerical examples demonstrate the validity and accuracy of the proposed method.

关键词： BIW structure Concept design TSMM Cross-sectional optimization MATLAB toolbox distributed parallel computing

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Voltage Risk Assessment of Distribution Network with Photovoltaic Intergration Based on parallel computing 2

Voltage Risk Assessment of Distribution Network with Photovo...

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2nd IEEE Conference on Energy Internet and Energy System Integration (EI2)

作者： Zhao, Yue Liu, Zhong Yu, Xiang Zhang, Chen Tang, Haibo State Grid Yangzhou Power Supply Co Yangzhou 225012 Jiangsu Peoples R China Southeast Univ Sch Elect Engn Nanjing Jiangsu Peoples R China

ISBN: (纸本)9781538685495

Voltage fluctuations in distribution networks are usually caused by the stochastic volatility of photovoltaic generation system and load. The traditional deterministic power flow calculation method is difficult to assess the voltage risk. Moreover, traditional serial computing technologies cannot provide rapid voltage risk assessment of large-scale distribution networks. To address these problems, the probabilistic characteristics of PV generation and load fluctuations are first analyzed. Then, the corresponding probabilistic model is established based on the Newton-Raphson algorithm. Finally, an indicator to evaluate voltage risk is proposed by using the Monte-Carlo simulation. In order to meet the computing speed requirement imposed by large-scale distribution networks, a parallel computing platform based on Apache Spark is designed, and a parallel implementation of the Monte-Carlo simulation on Spark Resilience distributed Datasets (RDD) is established. Simulation results based on real-world data illustrate the effectiveness of the proposed voltage risk assessment for large-scale distribution power networks and its computational efficiency.

关键词： Active distribution network distributed parallel computing Monte-Carlo simulation Voltage risk assessment

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Herring: Rethinking the Parameter Server at Scale for the Cloud

Herring: Rethinking the Parameter Server at Scale for the Cl...

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International Conference on High Performance computing, Networking, Storage and Analysis (SC)

作者： Thangakrishnan, Indu Cavdar, Derya Karakus, Can Ghai, Piyush Selivonchyk, Yauheni Pruce, Cory Amazon Web Serv Seattle WA 98109 USA

ISBN: (纸本)9781728199986

Training large deep neural networks is timeconsuming and may take days or even weeks to complete. Although parameter-server-based approaches were initially popular in distributed training, scalability issues led the field to move towards all -reduce -based approaches. Recent developments in cloud networking technologies, however, such as the Elastic Fabric Adapter (EFA) and Scalable Reliable Datagram (SRD), motivate a re -thinking of the parameter-server approach to address its fundamental inefficiencies. To this end, we introduce a novel communication library, Herring, which is designed to alleviate the performance bottlenecks in parameter-server-based training. We show that gradient reduction with Herring is twice as fast as all -reduce -based methods. We further demonstrate that training deep learning models like BERTiarge using Herring outperforms all -reduce -based training, achieving 85% scaling efficiency on large clusters with up to 2048 MINA V100 GPUs without accuracy drop.

关键词： Deep Learning Data parallel Training Scalability distributed parallel computing

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Iterative Mapreduce MPI Oil Reservoir Simulator 10

Iterative Mapreduce MPI Oil Reservoir Simulator

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10th International Conference on Software Technologies (ICSOFT)

作者： Mansurova, Madina Akhmed-Zaki, Darkhan Shomanov, Adai Matkerim, Bazargul Alimzhanov, Ermek al Farabi Kazakh Natl Univ Dept Comp Sci Alma Ata Kazakhstan

ISBN: (纸本)9789897581397

Paper presents an advanced Iterative MapReduce MPI oil reservoir simulator. First we present an overview of working implementations that make use of the same technologies. Then we define an academic example of numeric problem with an emphasis on its computational features. We present a distributed parallel algorithm of hybrid solution of the problem using MapReduce Hadoop and MPI technologies and describe an improved variant of the algorithm using memory-mapped files.

关键词： MapReduce MPI distributed parallel computing Memory-mapped Files

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