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A metaheuristic based on fusion and fission for partitioning problems 06

A metaheuristic based on fusion and fission for partitioning...

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International symposium on parallel and distributed processing (IPDPS)

作者： C.-E. Bichot Laboratoire d'Optimisation Globale (LOG) DSNA-DTI - ENAC FRANCE

ISBN: (纸本)9781424400546

Metaheuristics are very useful methods because they can find (approximate) solutions of a great variety of problems. One of them, which interests us, is graph partitioning. We present a new metaheuristic based on nuclear fusion and fission of atoms. This metaheuristic, called fusion fission, is compared to other classical algorithms. First, we present spectral and multilevel algorithms which are used to solve partitioning problems. Secondly, we present two metaheuristics applied to partitioning problems: simulated annealing and ant colony algorithms. We show that fusion fission gives good results, compared to the other algorithms. We demonstrate on a problem of air traffic control that metaheuristics methods can give better results than specific methods

关键词： Partitioning algorithms Fusion reactors Simulated annealing Air traffic control parallel processing Very large scale integration Image segmentation Automotive components Genetic algorithms Minimization methods

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parallel implementation and performance characterization of MUSCLE 06

Parallel implementation and performance characterization of ...

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International symposium on parallel and distributed processing (IPDPS)

作者： Xi Deng Eric Li Jiulong Shan Wenguang Chen Department of Computer Science Tsinghua University Beijing China Intel China Research Center Limited Beijing China

ISBN: (纸本)9781424400546

Multiple sequence alignment is a fundamental and very computationally intensive task in molecular biology. MUSCLE, a new algorithm for creating multiple alignments of protein sequences, achieves a highest rank in accuracy and the fastest speed compared to ClustalW as well as T-Coffee, some widely used tools in multiple sequence alignment. To further accelerate the computations, we present the parallel implementation of MUSCLE in this paper. It is decomposed into several independent modules, which are parallelized with different OpenMP paradigms. We also conduct detailed performance characterization on symmetric multiple processor systems. The experiments show that MUSCLE scales well with the increase of processors, and achieves up to 15./spl times/ speedup on 16-way shared memory multiple processor system.

关键词： Muscles Sequences Biology computing Proteins Concurrent computing Iterative algorithms Computer science Acceleration Computational biology Phylogeny

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On-chip and on-line self-reconfigurable adaptable platform: the non-uniform cellular automata case 06

On-chip and on-line self-reconfigurable adaptable platform: ...

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International symposium on parallel and distributed processing (IPDPS)

作者： A. Upegui E. Sanchez Logic Systems Laboratory Ecole Polytechnique Fédérale de Lausanne Lausanne Switzerland

ISBN: (纸本)9781424400546

In spite of the high parallelism exhibited by cellular automata architectures, most implementations are usually run in software. For increasing execution parallelism, hardware implementations on FPGAs have been proposed, under the cost of being un-flexible, and inefficient in terms of resource utilization. In this paper, we present a platform for evolving CA by exploiting the partial re-configurability of current commercial FPGAs. Our implementation includes an on-chip soft-processor that generates a partial bitstream, reconfigures the FPGA, and computes the fitness. After finding a good individual, the evolved CA can be used as a peripheral for performing useful computation. As case study we present CA co-evolution for a random number generator and for the firefly synchronization problem

关键词： Computer aided software engineering Hardware Field programmable gate arrays Circuits Genomics Bioinformatics Programmable logic arrays System-on-a-chip parallel processing Costs

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MT-ClustalW: multithreading multiple sequence alignment 06

MT-ClustalW: multithreading multiple sequence alignment

引用

International symposium on parallel and distributed processing (IPDPS)

作者： K. Chaichoompu S. Kittitornkun S. Tongsima Department of Computer Engineering Faculty of Engineering King Mongkut''s Institute of Technology Bangkok Thailand National Center for Genetic Engineering and Biotechnology Klong Luang Pathum Thani Thailand

ISBN: (纸本)9781424400546

ClustalW is the most widely used tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three stages: pairwise alignment, guide tree generation and progressive alignment. This paper analyzes and enhances a multithreaded implementation of ClustalW called ClustalW-SMP for higher throughput. Our goal is to maximize the degree of parallelism on multithreading ClustalW called MultiThreading-ClustalW (MT-ClustalW). As a result, bioinformatics laboratories are able to use this MT-ClustalW with much less energy consumption on multicore and SMP (symmetric multiprocessor) machines than that of PC clusters. The experiment results show that the MT-ClustalW framework can achieve a considerable speedup over the sequential ClustalW and original multithreaded ClustalW-SMP implementations

关键词： Multithreading Genetic engineering Workstations Throughput parallel processing Bioinformatics Proteins Concurrent computing Dynamic scheduling Biotechnology

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Chedar: peer-to-peer middleware 06

Chedar: peer-to-peer middleware

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International symposium on parallel and distributed processing (IPDPS)

作者： A. Auvinen M. Vapa M. Weber N. Kotilainen J. Vuori Department of Mathematical Information Technology University of Jyväskylä Finland

ISBN: (纸本)9781424400546

In this paper we present a new peer-to-peer (P2P) middleware called CHEap distributed ARchitecture (Chedar). Chedar is totally decentralized and can be used as a basis for P2P applications. Chedar tries to continuously optimize its overlay network topology for maximum performance. Currently Chedar combines four different topology management algorithms and provides functionality to monitor how the peer-to-peer network is self-organizing. It also contains basic search algorithms for P2P resource discovery. Chedar has been used for building a data fusion prototype and a P2PDisCo distributed computing application, which provides an interface for distributing the computation of Java applications. To allow Chedar to be used in mobile devices, the Mobile Chedar middleware has also been developed

关键词： Peer to peer computing Middleware Network topology distributed computing Computer network management Monitoring Prototypes Computer applications Computer interfaces Java

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Checkpointing and rollback-recovery protocol for mobile systems with MW session guarantee 06

Checkpointing and rollback-recovery protocol for mobile syst...

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International symposium on parallel and distributed processing (IPDPS)

作者： J. Brzezinski A. Kobusinska M. Szychowiak Institute of Computing Science Poznań University of Technology Poznan Poland

ISBN: (纸本)9781424400546

In the mobile environment, weak consistency replication of shared data is the key to obtaining high data availability, good access performance, and good scalability. Therefore new class of consistency models, called session guarantees, recommended for mobile environment, has been introduced. Session guarantees, called also client-centric consistency models, have been proposed to define required properties of the system regarding consistency from the client's point of view. Unfortunately, none of proposed consistency protocols providing session guarantees is resistant to server failures. Therefore, in this paper checkpointing and rollback-recovery protocol rVsMW, which preserves monotonic writes session guarantee is presented. The recovery protocol is integrated with the underlying consistency protocol by integrating operations of taking checkpoints with coherence operations of VsSG protocol.

关键词： Checkpointing Protocols Mobile computing Availability File servers Scalability Switches Fault tolerance distributed computing Mobile radio mobility management

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A configurable framework for stream programming exploration in baseband applications 06

A configurable framework for stream programming exploration ...

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International symposium on parallel and distributed processing (IPDPS)

作者： J. Bengtsson B. Svensson Centre for Research on Embedded Systems Halmstad University Halmstad Sweden

ISBN: (纸本)9781424400546

This paper presents a configurable framework to be used for rapid prototyping of stream based languages. The framework is based on a set of design patterns defining the elementary structure of a domain specific language for high-performance signal processing. A stream language prototype for baseband processing has been implemented using the framework. We introduce language constructs to efficiently handle dynamic reconfiguration of distributed processing parameters. It is also demonstrated how new language specific primitive data types and operators can be used to efficiently and machine independently express computations on bitfields and data-parallel vectors. These types and operators yield code that is readable, compact and amenable to a stricter type checking than is common practice. They make it possible for a programmer to explicitly express parallelism to be exploited by a compiler. In short, they provide a programming style that is less error prone and has the potential to lead to more efficient implementations

关键词： Baseband Prototypes parallel processing Base stations Signal processing Programming profession Application software Computer architecture Computer languages Multiaccess communication

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Reconfigurable communications for image processing applications 06

Reconfigurable communications for image processing applicati...

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International symposium on parallel and distributed processing (IPDPS)

作者： A.B. Soares L. Carro A.A. Susin Instituto de Informática Universidade Federal do Rio Grande do Sul Porto Alegre Brazil

ISBN: (纸本)9781424400546

This work tries to reuse programmable communication resources like a network-on-chip (NoC) in the acceleration of image applications. We show a mathematical model for the computation and communication pattern of two distributed motion estimation algorithms, full search block matching algorithm and multi-resolution block matching algorithm. Experimental results show that the use of the multi-resolution method reduces not only the computation time but also the traffic of messages on the NoC. This leads to a lower power consumption in the NoC during the processing time of each image. The studied examples show the importance of the link between algorithms and their mapping onto a programmable fabric, not only regarding computation, but facing communication as well

关键词： Image processing Network-on-a-chip Pattern matching Acceleration Mathematical model distributed computing Motion estimation Traffic control Energy consumption Fabrics

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Adaptability management and deterministic scheduling of media flows on parallel storage servers 06

Adaptability management and deterministic scheduling of medi...

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International symposium on parallel and distributed processing (IPDPS)

作者： C. Mourlas Department of Comunication andMedia Studies University of Athens (NKUA) Athens Greece

ISBN: (纸本)9781424400546

We study a new design strategy for the implementation of parallel media servers with a predictable behavior. This strategy makes the timing properties and the quality of presentation of a set of media streams predictable. The proposed strategy provides deterministic guarantees and service reliability for each stream that can't be compromised by server contention. Our real-time scheduling approach exploits the performance of parallel environments and seems a promising method that brings the advantages of parallel computation in media servers. The proposed mechanism provides deterministic service for both constant bit rate (CBR) and variable bit rate (VBR) streams. We present an efficient placement strategy for data frames as well as an adaptability strategy that allows appropriate frames to be dropped without sacrificing the ability to present multimedia applications predictably in time. A prototype implementation of the proposed parallel media server illustrates the concepts of server allocation and scheduling of continuous media streams

关键词： Streaming media Computer architecture Timing Bit rate Resource management Information retrieval Network servers Processor scheduling Concurrent computing Prototypes

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A multiprocessor architecture for the massively parallel model GCA 06

A multiprocessor architecture for the massively parallel mod...

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International symposium on parallel and distributed processing (IPDPS)

作者： W. Heenes R. Hoffmann J. Jendrsczok TU Darmstadt FB Informatik FG Rechnerarchitektur Darmstadt Germany

ISBN: (纸本)9781424400546

The GCA (global cellular automata) model consists of a collection of cells which change their states synchronously depending on the states of their neighbors like in the classical CA model. In differentiation to the CA model the neighbors are not fixed and local, they are variable and global. The GCA model is applicable to a wide range of parallel algorithms. In this paper, a multiprocessor architecture for the massively parallel GCA model is presented. In contrast to a special purpose implementation of a GCA algorithm the multiprocessor system allows the implementation in a flexible way through programming. The architecture mainly consists of a number of cell processors and a network. The cell processors are dedicated RISC processors, the network is a crossbar implemented with multiplexers. Only read-accesses through the network are necessary in the GCA model leading to a simplified structure. A system with 32 processors was implemented as a prototype on a FPGA. The analysis and implementation results have shown that the performance of the system scales very well with the number of processors

关键词： Computer architecture Hardware Field programmable gate arrays parallel architectures parallel algorithms Multiprocessing systems Reduced instruction set computing Multiplexing Prototypes Performance analysis

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