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5th Pacific Rim Conference on Multimedia, PCM 2004

作者： Yang, Chao-Tung Wang, Ko-Tzu Li, Kuan-Ching Lee, Liang-Teh High Performance Computing Laboratory Dept. of Computer Science and Information Engineering Tunghai University Taichung407 Taiwan Parallel and Distributed Processing Center Dept. of Computer Science and Information Management Providence University Taichung433 Taiwan Dept. of Computer Science and Engineering Tatung University Taipei104 Taiwan

ISBN: (纸本)9783540239772

In this research paper, we integrate and implement High-Availability (HA) and Load-Balancing technologies to clusters of workstations, increasing both the availability and scalability of services and resources in these systems. The cluster of workstations is commonly built and used as web-based VOD servers. Thus, this paper presents the hardware and software configurations of cluster systems working as VOD servers. © Springer-Verlag Berlin Heidelberg 2004.

关键词： Cluster computing

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A science gateway getting ready for serving the international molecular simulation community 2

A science gateway getting ready for serving the internationa...

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2012 EGI Community Forum / EMI 2nd Technical Conference, EGICF-EMITC 2012

作者： Gesing, Sandra Herres-Pawlis, Sonja Birkenheuer, Georg Brinkmann, André Grunzke, Richard Kacsuk, Peter Kohlbacher, Oliver Kozlovszky, Miklos Krüger, Jens Müller-Pfefferkorn, Ralph Schäfer, Patrick Steinke, Thomas Center for Bioinformatics Department of Computer Science University of Tübingen Sand 14 Tübingen72076 Germany Department of Chemistry Ludwig-Maximilians-University Munich Butenandtstr. 5-13 München81377 Germany Paderborn Center for Parallel Computing University of Paderborn Warburger Str. 100 Paderborn33089 Germany Johannes Gutenberg-University Mainz Mainz55099 Germany Center for Information Services and High Performance Computing Technische Universität Dresden Zellescher Weg 12-14 Germany Laboratory of Parallel and Distributed Systems MTA SZTAKI Kende Street 13-17 Budapest1111 Hungary Zuse Institute Berlin Takustraße 7 Berlin14195 Germany

The project MoSGrid (Molecular Simulation Grid) has been developing a web-based science gateway supporting the community with various services for quantum chemistry, molecular modeling, and docking. Users gain access to distributed computing infrastructures (DCIs) via intuitive user interfaces for sophisticated tools, specialized workflows, and distributed repositories. Currently, the MoSGrid community consists of about 120 users from a number of fields related to chemistry and bioinformatics located in Germany. However, the underlying security infrastructure is generally applicable and can be deployed in arbitrary projects. MoSGrid intends to address the international community by participating in the EU-projects SCI-BUS (Scientific gateway Based User Support) and ER-flow (Building an European Research Community through Interoperable Workflows and Data), and collaborating with the EU-project EDGI (European Desktop Grid Initiative). © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.

关键词： Quantum chemistry

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A high-performance computational resource broker for grid computing environments

A high-performance computational resource broker for grid co...

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International Conference on Advanced Information Networking and Applications (AINA)

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

ISBN: (纸本)0769522491

Internet computing and grid technologies promise to change the way we tackle complex problems. They will enable large-scale aggregation and sharing of computational, data and other resources across institutional boundaries. As grid computing is becoming a reality, there is a need for managing and monitoring the available resources worldwide, as well as the need for conveying these resources to the everyday user. This paper describes a resource broker with its main function as to match the available resources to the user's needs. The use of the resource broker provides a uniform interface to access any of the available and appropriate resources using user's credentials. The resource broker runs on top of the Globus toolkit. Therefore, it provides security and current information about the available resources and serves as a link to the diverse systems available in the grid.

关键词： Grid computing Resource management Bandwidth distributed computing Network servers Monitoring Information security Middleware Access protocols Java

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parallel global routing algorithms for standard cells

Parallel global routing algorithms for standard cells

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International Symposium on parallel Processing

作者： Z. Xing J. Chandy P. Banerjee Computer and Systems Research Laboratory University of Illinois Urbana IL USA Cadence Design Systems Chelmsford MA USA Center for Parallel and Distributed Computing Northwestern University Evanston IL USA

In this paper, we propose three different parallel algorithms based on a state-of-the-art global router called TimberWolfSC. The parallel algorithms have been implemented by using the Message Passing Interface (MPI), and have been evaluated on a wide range of parallel platforms such as the Sun Sparccenter 1000 and the Intel Paragon. Our experimental results show good speedups and qualities from two of these parallel algorithms. We have been able to reduce runtimes of some circuits from half an hour to 5 minutes, obtained speedups of about 4.0 to 5.0 on 8 processors, with less than 2-3% degradation of quality of the solutions.

关键词： Routing parallel algorithms distributed computing Message passing Pins Wire Contracts Concurrent computing Laboratories Sun

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Data management for large‐scale scientific computations in high performance distributed systems

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Cluster computing 2000年第1期3卷 45-60页

作者： Choudhary, A. Kandemir, M. No, J. Memik, G. Shen, X. Liao, W. Nagesh, H. More, S. Taylor, V. Thakur, R. Stevens, R. Center for Parallel and Distributed Computing Department of Electrical and Computer Engineering Northwestern University Evanston USA Department of Computer Science and Engineering The Pennsylvania State University University Park USA Mathematics and Computer Science Division Argonne National Laboratory Argonne USA

With the increasing number of scientific applications manipulating huge amounts of data, effective high-level data management is an increasingly important problem. Unfortunately, so far the solutions to the high‐level data management problem either require deep understanding of specific storage architectures and file layouts (as in high-performance file storage systems) or produce unsatisfactory I/O performance in exchange for ease-of-use and portability (as in relational DBMSs). In this paper we present a novel application development environment which is built around an active meta-data management system (MDMS) to handle high-level data in an effective manner. The key components of our three-tiered architecture are user application, the MDMS, and a hierarchical storage system (HSS). Our environment overcomes the performance problems of pure database-oriented solutions, while maintaining their advantages in terms of ease-of-use and portability. The high levels of performance are achieved by the MDMS, with the aid of user-specified, performance-oriented directives. Our environment supports a simple, easy-to-use yet powerful user interface, leaving the task of choosing appropriate I/O techniques for the application at hand to the MDMS. We discuss the importance of an active MDMS and show how the three components of our environment, namely the application, the MDMS, and the HSS, fit together. We also report performance numbers from our ongoing implementation and illustrate that significant improvements are made possible without undue programming effort.

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DrugProtKGE: Weakly Supervised Knowledge Graph Embedding for Highly-Effective Drug-Protein Interaction Representation

DrugProtKGE: Weakly Supervised Knowledge Graph Embedding for...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Qiu, Yanlong Wang, Siqi Yang, Xi Qiu, Xinyuan Wu, Chengkun Cui, Yingbo Yang, Canqun National University of Defense Technology Institute for Quantum Information State Key Laboratory of High-Performance Computing College of Computer Science Hunan Changsha410073 China National Supercomputer Center in Tianjin Tianjin300457 China National University of Defense Technology National Key Laboratory of Parallel and Distributed Computing College of Computer Science Hunan Changsha410073 China National University of Defense Technology Department of Biology and Chemistry College of Science Hunan Changsha410073 China

ISBN: (纸本)9798350337488

With the exponential growth of biomedical knowledge in unstructured text repositories such as PubMed, it is imminent to establish a knowledge graph-style, efficient searchable and targeted database that can support the need of information retrieval from researchers and clinicians. To mine knowledge from graph databases, most previous methods view a triple in a graph (see Fig. 1) as the basic processing unit and embed the triplet element (i.e. drugs/chemicals, proteins/genes and their interaction) as separated embedding matrices, which cannot capture the semantic correlation among triple elements. To remedy the loss of semantic correlation caused by disjoint embeddings, we propose a novel approach to learn triple embeddings by combining entities and interactions into a unified representation. Furthermore, traditional methods usually learn triple embeddings from scratch, which cannot take advantage of the rich domain knowledge embedded in pre-trained models, and is also another significant reason for the fact that they cannot distinguish the differences implied by the same entity in the multi-interaction triples. In this paper, we propose a novel fine-tuning based approach to learn better triple embeddings by creating weakly supervised signals from pre-trained knowledge graph embeddings. The method automatically samples triples from knowledge graphs and estimates their pairwise similarity from pre-trained embedding models. The triples are then fed pairwise into a Siamese-like neural architecture, where the triple representation is fine-tuned in the manner bootstrapped by triple similarity scores. Finally, we demonstrate that triple embeddings learned with our method can be readily applied to several downstream applications (e.g. triple classification and triple clustering). We evaluated the proposed method on two open-source drug-protein knowledge graphs constructed from PubMed abstracts, as provided by BioCreative. Our method achieves consistent improvement in both t

关键词： Drug-Protein Interaction Knowledge Graph Embedding Triple Embedding Weakly Supervised Learning

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A novel application development environment for large-scale scientific computations 00

A novel application development environment for large-scale ...

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Proceedings of the 14th international conference on Supercomputing

作者： X. Shen W. Liao A. Choudhary G. Memik M. Kandemir S. More G. Thiruvathukal A. Singh Center for Parallel and Distributed Computing Department of Electrical and Computer Engineering Northwestern University Evanston IL Department of Computer Science and Engineering The Pennsylvania State University University Park PA School of Computing Telecommunications and Information Sciences JHPC Laboratory Depaul University

Our results demonstrate that our novel application development environment provides both ease-of-use and high performance for large-scale, I/O-intensive scientific applications.

ISBN: (纸本)9781581132700

Our results demonstrate that our novel application development environment provides both ease-of-use and high performance for large-scale, I/O-intensive scientific applications.

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An enhanced parallel loop self-scheduling scheme for cluster environments

An enhanced parallel loop self-scheduling scheme for cluster...

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International Conference on Advanced Information Networking and Applications (AINA)

作者： Chao-Tung Yang Kuan-Wei Cheng 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)0769522491

In this paper, a parallel loop self-scheduling scheme for heterogeneous PC cluster systems is proposed. Though the proposed scheme does allow users to choose parameters before the execution initialization phase, there are still weaknesses that motivate us to go further with new improvements in that scheme. For instance, a decision on a fixed and monotonous parameter can easily lead to invalid schedule by using previous input information. Thus, it is proposed in this paper a new scheme, where the scheduling parameter can be adjusted dynamically and fit into most widely available computer systems, in order to provide higher overall performance.

关键词： Processor scheduling Dynamic scheduling Load management Master-slave Concurrent computing distributed computing Clustering algorithms Runtime Computer science Scheduling algorithm

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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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RAFlow: Read Ahead Accelerated I/O Flow through Multiple Virtual Layers

RAFlow: Read Ahead Accelerated I/O Flow through Multiple Vir...

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International Conference on Networking, Architecture, and Storage (NAS)

作者： Zhaoning Zhang Kui Wu Huiba Li Jinghua Feng Yuxing Peng Xicheng Lu National Key Laboratory for Parallel and Distributed Processing National University of Defense Technology China Computer Science Department University of Victoria B.C. Canada National Super Computing Center Tianjin China

Virtualization is the foundation for cloud computing, and the virtualization can not be achieved without software defined, elastic, flexible and scalable virtual layers. Unfortunately, if multiple virtual storage devices are chained together, the system may be subject to severe performance degradation. While the read-ahead (RA) mechanism in storage devices plays a very important role to improve I/O performance, RA may not be effective as expected for multiple virtualization layers, since it is originally designed for one layer only. When I/O requests are passed through a long I/O path, they may trigger a chain reaction and lead to unnecessary data transmission and thus bandwidth waste. In this paper, we study the dynamic behavior of RA through multiple I/O layers and demonstrate that if controlled well, RA can greatly accelerate I/O speed. We present RAFlow, a RA control mechanism, to effectively improve I/O performance by strategically expanding RA window at each layer. Our real-world experiments show that it can achieve 20% to 50% performance improvement in I/O paths with up to 8 virtualized storage devices.

关键词： Radio access networks Acceleration distributed databases Performance evaluation Synchronization Benchmark testing Degradation

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