Enabling e-Science Applications on the Cloud with COMPSs

  • Daniele Lezzi
  • Roger Rafanell
  • Abel Carrión
  • Ignacio Blanquer Espert
  • Vicente Hernández
  • Rosa M. Badia
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7155)

Abstract

COMP Superscalar (COMPSs) is a programming framework that provides an easy-to-use programming model and a runtime to ease the development of applications for distributed environments. Thanks to its modular architecture COMPSs can use a wide range of computational infrastructures providing a uniform interface for job submission and file transfer operations through adapters for different middlewares. In the context of the VENUS-C project the COMPSs framework has been extended through the development of a programming model enactment service that allows researcher to transparently port and execute scientific applications in the Cloud.

This paper presents the implementation of a bioinformatics workflow (using BLAST as core program), the porting to the COMPSs framework and its deployment on the VENUS-C platform. The proposed approach has been evaluated on a Cloud testbed using virtual machines managed by EMOTIVE Cloud and compared to a similar approach on the Azure platform and to other implementations on HPC infrastructures.

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References

  1. 1.
    Tejedor, E., Badia, R.M.: COMP Superscalar: Bringing GRID superscalar and GCM Together. In: 8th IEEE International Symposium on Cluster Computing and the Grid (May 2008)Google Scholar
  2. 2.
    Lezzi, D., Rafanell, R., Badia, R.M., Lordan, F., Tejedor, E.: COMPSs in the VENUS-C Platform: enabling e-Science applications on the Cloud. In: Proc. of the IBERGRID 2011 Conf., Santander (June 2011)Google Scholar
  3. 3.
    Foster, I., et al.: OGSA Basic Execution Service Version 1.0. Grid Forum Document GFD-RP. 108 (August 8, 2007)Google Scholar
  4. 4.
    Savva, A. (ed.): Job Submission Description Language (JSDL) Specification, Version 1.0. Grid Forum Document GFD-R.056 (November 7, 2005)Google Scholar
  5. 5.
    Simmhan, Y., van Ingen, C.: Bridging the Gap between Desktop and the Cloud for eScience Applications, Microsoft Research, U.S. (2010), http://research.microsoft.com/pubs/118329/Simmhan2010CloudSciencePlatform.pdf
  6. 6.
    Open Nebula, http://opennebula.org
  7. 7.
    Goiri, I., Guitart, J., Torres, J.: Elastic Management of Tasks in Virtualized Environments. In: XX Jornadas de Paralelismo, JP 2009, A Corua, Spain, September 16-18, pp. 671–676 (2009)Google Scholar
  8. 8.
    Open Cloud Computing Interface Working Group, http://www.occi-wg.org
  9. 9.
    Distributed Management Task Force Inc., Open Virtualization Format Specification v1.1, DMTF Standard DSP0243 (2010)Google Scholar
  10. 10.
  11. 11.
    Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. Journal of Molecular Biology 215(3), 403–410 (1990), doi:10.1006/jmbi.1990.9999Google Scholar
  12. 12.
    Darling, A., Carey, L., Feng, W.: The Design, Implementation, and Evaluation of mpiBLAST. In: Proc. of the 4th Intl. Conf. on Linux Clusters (2003)Google Scholar
  13. 13.
    Matsunaga, A., Tsugawa, M., Fortes, J.: CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications. In: IEEE Fourth International Conference on eScience (2008)Google Scholar
  14. 14.
    Dean, J., Ghemawat, S.: MapReduce: Simplified Data Processing on Large Clusters. In: Proc. of the 6th Symp. on Operating Systems Design & Implementation, pp.137–150 (2004)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Daniele Lezzi
    • 1
    • 2
  • Roger Rafanell
    • 1
  • Abel Carrión
    • 4
  • Ignacio Blanquer Espert
    • 4
  • Vicente Hernández
    • 4
  • Rosa M. Badia
    • 1
    • 3
  1. 1.Barcelona Supercomputing Center, Centro Nacional de Supercomputación (BSC-CNS)Spain
  2. 2.Universitat Politècnica de Catalunya (UPC)Spain
  3. 3.Spanish Council for Scientific Research (CSIC)Artificial Intelligence Research Institute (IIIA)Spain
  4. 4.Instituto de Instrumentación para Imagen Molecular (I3M), Centro mixto CSICUniversitat Politècnica de València, CIEMATSpain

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