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BLAST Distributed Execution on Partitioned Databases with Primary Fragments

  • Conference paper
High Performance Computing for Computational Science - VECPAR 2008 (VECPAR 2008)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5336))

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Abstract

BLAST is one of the most popular computational biology tools. The execution cost of BLAST is highly dependent on database sizes, which have considerably increased following all recent advances in sequencing methods. The evaluation of BLAST in distributed and parallel environments like PC clusters and Grids has been largely investigated in order to obtain better performances. This work evaluates a replicated allocation of the (sequences) database, where each copy is also physically fragmented. We investigate two dynamic workload balancing methods that focus on our database allocation strategy. Preliminary practical results show that we achieve both a balanced workload and very good performances. We briefly discuss ideas that would make our approach feasible for Grid computational environments.

Work partially funded by CNPq-INRIA (GriData project).

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Author information

Authors and Affiliations

  1. PUC-Rio Dep Informatica, Rio de Janeiro, Brazil

    Daniel Xavier de Sousa & Sergio Lifschitz

  2. LINA and INRIA, Nantes, France

    Patrick Valduriez

Authors
  1. Daniel Xavier de Sousa
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  2. Sergio Lifschitz
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  3. Patrick Valduriez
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Editor information

Editors and Affiliations

  1. Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal

    José M. Laginha M. Palma

  2. University of Toulouse, INP (ENSEEIHT), IRIT, 2 rue Charles-Camichel, 31071, Toulouse CEDEX 7, France

    Patrick R. Amestoy

  3. University of Toulouse, INP (ENSEEIHT); IRIT, rue Charles-Camichel, 31071, Toulouse CEDEX 7, France

    Michel Daydé

  4. Federal University of Rio de Janeiro, P.O. Box 68511, 21941-972, Rio de Janeiro, RJ, Brazil

    Marta Mattoso

  5. Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal

    João Correia Lopes

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© 2008 Springer-Verlag Berlin Heidelberg

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de Sousa, D.X., Lifschitz, S., Valduriez, P. (2008). BLAST Distributed Execution on Partitioned Databases with Primary Fragments. In: Palma, J.M.L.M., Amestoy, P.R., Daydé, M., Mattoso, M., Lopes, J.C. (eds) High Performance Computing for Computational Science - VECPAR 2008. VECPAR 2008. Lecture Notes in Computer Science, vol 5336. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-92859-1_48

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  • DOI: https://doi.org/10.1007/978-3-540-92859-1_48

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-92858-4

  • Online ISBN: 978-3-540-92859-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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