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检索条件"机构=Distributed and High Performance Computing Research Group Department of Computer Science"

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Implementation and evaluation of a Java based computational grid for bioinformatics applications

Implementation and evaluation of a Java based computational ...

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International Conference on Advanced Information Networking and Applications (AINA)

作者： Chao-Tung Yang Yi-Chun Hsiung Heng-Chuan Kan High-Performance Computing Laboratory Department of Computer Science and Information Engineering Tunghai University Taichung Taiwan Biotechnology Group South Region Office National Center of High-performance Computing Tainan Taiwan

ISBN: (纸本)0769522491

In the present study, THUBioGrid, an experimental distributed computing application for bioinformatics (BioGrid) is proposed. THUBioGrid incorporates directory services (data and software), grid computing methods (security, authentication, data transport and remote jobs), and gene sequence/genomic data processing methods. It uses Java CoG Kit plus bioinformatics Java packages to perform various computational tasks. The performance of THUBioGrid has been tested by executing the FASTA and mpiBLAST programs for protein sequence alignment applications. Results demonstrate the speed-up effects with increasing number of processors used in the computations.

关键词： Java Grid computing Bioinformatics Application software distributed computing Data security Authentication Genomics Data processing Packaging

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On implementation of an enhanced and integrated parallel programming Web-based toolkit

On implementation of an enhanced and integrated parallel pro...

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International Conference on Information Technology: research and Education (ITRE)

作者： Kuan-Ching Li Chao-Tung Yang Parallel and Distributed Processing Center Department of Computer Science and Information Management Providence University Taichung Taiwan High Performance Computing Laboratory Department of Computer Science and Infnmation Engineering Tunghai University Taichung Taiwan

ISBN: (纸本)0780389328

The computing power provided by high performance and low cost PC-based clusters and grid computing platforms are attractive and they are equal or superior to supercomputers and mainframes. In parallel, discussions on how to obtain more computing power from these computing platforms become an interesting issue. The development of applications for these high-performance computing platforms is complicated for several reasons: the complexity of applications themselves, which combines aspects of super computing and distributed computing, and by the need to achieve higher performance. This paper describes the design rationale and implementation of a parallel programming Web-based toolkit, to ease the parallel programming learning process, with the use of Web-based interface. The toolkit has widely been used in MPI parallel programming courses (both in graduate and undergraduate levels) and industry trainings.

关键词： Parallel programming Concurrent computing Application software distributed computing Grid computing high performance computing Visualization computer science Supercomputers Industrial training

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The anatomy of a course in cluster and grid computing

The anatomy of a course in cluster and grid computing

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International Conference on Information Technology: research and Education (ITRE)

作者： Chao-Tung Yang Kuan-Ching Li High Performance Computing Laboratory Department of Computer Science and Information Engineering Tunghai University Taichung Taiwan Parallel and Distributed Processing Center Department of Computer Science and Information Management Providence University Taichung Taiwan

ISBN: (纸本)0780389328

Cluster and grid computing is a relatively new interdisciplinary field, where computer science, engineering and computational biology are its core supporting disciplines. The rise of cluster and grid computing discipline brings to computer science faculty members new opportunities and challenges, both in education and in research. In this paper, we explore issues in teaching cluster and grid computing, the developing of curricula, and thoughts to foster student to work on research projects in cluster and grid computing.

关键词： Anatomy Grid computing distributed computing Concurrent computing computer networks Brain modeling Predictive models computer science Education Space technology

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Efficient subtorus processor allocation in a multi-dimensional torus

Efficient subtorus processor allocation in a multi-dimension...

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International Conference on high performance computing in the Asia-Pacific Region

作者： Weizhen Mao Jie Chen W. Watson Department of Computer Science College of William and Mary Williamsburg VA USA The High Performance Computing Group Jefferson Laboratory Newport News VA USA

Processor allocation in a mesh or torus connected multicomputer system with up to three dimensions is a hard problem that has received some research attention in the past decade. With the recent deployment of multicomputer systems with a torus topology of dimensions higher than three, which are used to solve complex problems arising in scientific computing, it becomes imminent to study the problem of allocating processors of the configuration of a torus in a multi-dimensional torus connected system. In this paper, we first define the concept of a semitorus. We present two partition schemes, the Equal Partition (EP) and the Non-Equal Partition (NEP), that partition a multi-dimensional semitorus into a set of sub-semitori. We then propose two processor allocation algorithms based on these partition schemes. We evaluate our algorithms by incorporating them in commonly used FCFS and backfilling scheduling policies and conducting simulation using workload traces from the Parallel Workloads Archive. Specifically, our simulation experiments compare four algorithm combinations, FCFS/EP, FCFS/NEP, backfilling/EP, and backfilling/NEP, for two existing multi-dimensional torus connected systems. The simulation results show that our algorithms (especially the backfilling/NEP combination) are capable of producing schedules with system utilization and mean job bounded slowdowns comparable to those in a fully connected multicomputer

关键词： Scheduling algorithm Processor scheduling Topology Partitioning algorithms Delay computer science Educational institutions high performance computing Scientific computing

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Implementation of a biology data translation system on grid environments

Implementation of a biology data translation system on grid ...

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International Conference on Information Technology: research and Education (ITRE)

作者： Chao-Tung Yang Yi-Chun Hsiung Heng-Chuan Kan Department of Computer Science and Infirmation Engineering Tunghai University Taichung Taiwan National Center for High-performance Computing Biotechnology Group South Region Office Shinshi Taiwan

ISBN: (纸本)0780389328

Biological data exists all over the world as various Web services, which provide biologists with much useful information. However, heterogeneous data formats present a technical hurdle for biologists to fully take advantage of the information. It needs some power tools to handle this issue. The grid technology could help common biology tools with high performance and high throughput. Even so, the data formats produced from various biology tools are heterogeneous. The process of information integration of heterogeneous biological data is complex and difficult. This paper describes an approach to solve this problem by using XML technologies combine with BioGrid system. We use BioJava to integrate with our system for translating data into XML format. Finally, an example is used to illustrate how these techniques can come together in integrating heterogeneous biological data sources.

关键词： XML Bioinformatics Databases Biology computing Grid computing Data analysis Genomics Biotechnology Proteins computer science

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Transparent resource allocation to exploit idle cluster nodes in computational grids

Transparent resource allocation to exploit idle cluster node...

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IEEE International Conference on e-science and Grid computing

作者： M.A.S. Netto R.N. Calheiros R.K.S. Silva C.A.R. De Rose C. Northfleet W. Cirne Department of Computer Science University of São Paulo Sao Paulo Brazil Research Center in High Performance Computing Porto Alegre Brazil Catholic University of Grande do Sul Porto Alegre Brazil Hewlett Packard Company Porto Alegre Brazil Federal University of Campina Grande Campina Grande Brazil

Clusters of workstations are one of the most suitable resources to assist e-scientists in the execution of large-scale experiments that demand processing power. The utilization rate of these machines is usually far from 100%, and hence this should motivate administrators to share their clusters to grid communities. However, exploiting these resources in computational grids is challenging and brings several problems. This paper presents a transparent resource allocation strategy to harness idle cluster resources aimed at executing grid applications. This novel approach does not make use of a formal allocation request to cluster resource managers. Moreover, it does not interfere with local cluster users, being non-intrusive, and hence motivating cluster administrators to publish their resources to grid communities. We present experimental results regarding the effects of the proposed strategy on the attendance time of both cluster and grid requests and we also analyze its effectiveness in clusters with different utilization rates

关键词： Resource management Grid computing high performance computing Workstations Large-scale systems Supercomputers computer science Instruments distributed computing Computational modeling

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CODACS prototype: CHIARA language and its compiler

CODACS prototype: CHIARA language and its compiler

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International Conference on distributed computing Systems Workshop

作者： L. Verdoscia M. Danelutto R. Esposito Institute for High Performance Computing and Networking National Research Council Napoli Italy Department of Computer Science University of Pisa Pisa Italy Research Centre On Software Technology University of Sannio Benevento Italy

We present CHIARA, the programming language used to program CODACS (a general purpose dataflow architecture exploiting FPGA technology), and describe the compiling strategies leading from CHIARA programs to the CODACS dataflow graphs. CHIARA is a functional programming language based on Backus'FP. We designed both the language and the compiling tools in such a way that CHIARA programs can be efficiently compiled and run onto the overall architecture and CODACS platform-processors being, for the latter, also the low-level (assembly) programming language. Some preliminary experimental results are discussed, demonstrating that the CHIARA approach to CODACS programming is feasible and promising.

关键词： Prototypes computer languages Field programmable gate arrays computer architecture Parallel processing Program processors high performance computing Functional programming Hardware Assembly

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Global and localized parallel preconditioning techniques for large scale solid Earth simulations

Global and localized parallel preconditioning techniques for...

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International Symposium on Parallel and distributed Processing (IPDPS)

作者： Kai Wang Sangbae Kim Jun Zhang K. Nakajima H. Okuda Laboratory for High Performance Scientific Computing and Computer Simulation Department of Computer Science University of Kentucky Lexington KY USA Research Organization for Information Science and Technology Meguro Tokyo Japan Department of Quantum Engineering and System Sciences University of Tokyo Bunkyo Tokyo Japan

We investigate and compare a few parallel preconditioning techniques in the iterative solution of large sparse linear systems arising from solid Earth simulation with and without using contact information in the domain partitioning process. Previous studies are focused on using static or matrix pattern based incomplete LU (ILU) preconditioners in a localized preconditioner implementation. Our current studies are concerned with preconditioner performance for solving two different cases with and without known contact information. For the cases with contact information, we use localized threshold value based incomplete LU (ILUT) preconditioner to improve efficiency. For the cases without contact information, we use a global sparse approximate inverse preconditioner with a static sparsity pattern to achieve robustness. Numerical results from simulating ground motion on a parallel supercomputer are given to compare the effectiveness of these parallel preconditioning techniques.

关键词： Large-scale systems Earth Solid modeling Linear systems Sparse matrices Computational modeling computer simulation Uniform resource locators Geoscience Information science

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Integrating MPI-based numerical software into an advanced parallel computing environment

Integrating MPI-based numerical software into an advanced pa...

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Euromicro Conference on Parallel, distributed and Network-Based Processing

作者： P. D'Ambra M. Danelutto D. di Serafino M. Lapegna Institute for High-Performance Computing and Networking (ICAR) National Research Council Naples Italy Department of Computer Science University of Pisa Pisa Italy Department of Mathematics Second University of Naples Caserta Italy Department of Mathematics and its Applications University of Naples Federico II Naples Italy

In this paper we present first experiences concerning the integration of MPI-based numerical software into an advanced programming environment for building parallel and distributed high-performance applications, which is under development in the context of Italian national research projects. Such a programming environment, named ASSIST, is based on a combination of the concepts of structured parallel programming and component-based programming. Some activities within the projects are devoted to the definition, implementation and testing of a methodology for the integration of a parallel numerical library into ASSIST. The goal is providing a set of efficient, accurate and reliable tools that can be easily used as building blocks for high-performance scientific applications. We focus on the integration of existing and widely used MPI-based numerical library modules. To this aim, we propose a general approach to embed MPI computations into the ASSIST basic programming unit. This approach has been tested using the MPICH implementation of MPI for networks of workstations. Some modifications have been applied to the MPICH process startup procedure, in order to make it compliant with the ASSIST environment. Results of experiments concerning the integration of routines from a well-known FFT package are discussed.

关键词： Parallel processing Programming environments Parallel programming Testing Libraries Buildings Application software Embedded computing Workstations Packaging

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Modeling of service-level agreements for composed services 13th

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13th IFIP/IEEE International Workshop on distributed Systems: Operations and Management, DSOM 2002

作者： Daly, David Kar, Gautam Sanders, William H. Center for Reliable and High-Performance Computing Coordinated Science Laboratory and Department of Electrical and Computer Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States IBM T.J. Watson Research Center P.O.Box 704 Yorktown HeightsNY10598 United States

ISBN: (纸本)3540000801

As Web services are increasingly accepted and used, the next step for them is the development of hierarchical and distributed services that can perform more complex tasks. In this paper, we focus on how to develop guarantees for the performance of an aggregate service based on the guarantees provided by the lower-level services. In particular, we demonstrate the problem with an example of an e-commerce Web site implemented using Web services. The example is based on the Transaction Processing performance Council (TPC) TPC-W Benchmark [8], which specifies an online store complete with a description of all the functionality of the site as well as a description of how customers use the site. We develop models of the site’s performance based on the performance of two sub-services. The model’s results are compared to experimental data and are used to predict the performance of the system under varying conditions. © Springer-Verlag Berlin Heidelberg 2002.

关键词： Web services

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