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Parallel Chaining Algorithms

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Recent Advances in the Message Passing Interface (EuroMPI 2010)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 6305))

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Abstract

Given a set of weighted hyper-rectangles in a k-dimensional space, the chaining problem is to identify a set of colinear and non-overlapping hyper-rectangles of total maximal weight. This problem is used in a number of applications in bioinformatics, string processing, and VLSI design. In this paper, we present parallel versions of the chaining algorithm for bioinformatics applications, running on multi-core and computer cluster architectures. Furthermore, we present experimental results of our implementations on both architectures.

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Authors and Affiliations

  1. Center for informatics sciences, Nile University, Smart Village, Giza, Egypt

    Mohamed Abouelhoda & Hisham Mohamed

Authors
  1. Mohamed Abouelhoda
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  2. Hisham Mohamed
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Editor information

Editors and Affiliations

  1. High Performance Computing Center Stuttgart (HLRS), Universität Stuttgart, Nobelstr. 19, 70569, Stuttgart, Germany

    Rainer Keller

  2. Parallel Software Technologies Laboratory, Department of Computer Science, University of Houston,  

    Edgar Gabriel

  3. High Performance Computing Center Stuttgart, University of Stuttgart, Nobelstr. 19, 70569, Stuttgart, Germany

    Michael Resch

  4. Department of Electrical Engineering and Computer Science, University of Tennessee, 37996-3450, Knoxville, TN, USA

    Jack Dongarra

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Abouelhoda, M., Mohamed, H. (2010). Parallel Chaining Algorithms. In: Keller, R., Gabriel, E., Resch, M., Dongarra, J. (eds) Recent Advances in the Message Passing Interface. EuroMPI 2010. Lecture Notes in Computer Science, vol 6305. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15646-5_15

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  • DOI: https://doi.org/10.1007/978-3-642-15646-5_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-15645-8

  • Online ISBN: 978-3-642-15646-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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