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.
Chapter PDF
Similar content being viewed by others
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
References
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)
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)
Foster, I., et al.: OGSA Basic Execution Service Version 1.0. Grid Forum Document GFD-RP. 108 (August 8, 2007)
Savva, A. (ed.): Job Submission Description Language (JSDL) Specification, Version 1.0. Grid Forum Document GFD-R.056 (November 7, 2005)
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
Open Nebula, http://opennebula.org
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)
Open Cloud Computing Interface Working Group, http://www.occi-wg.org
Distributed Management Task Force Inc., Open Virtualization Format Specification v1.1, DMTF Standard DSP0243 (2010)
SNIA CDMI, http://www.snia.org/tech_activities/standards/curr_standards/cdmi/
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.1990.9999
Darling, A., Carey, L., Feng, W.: The Design, Implementation, and Evaluation of mpiBLAST. In: Proc. of the 4th Intl. Conf. on Linux Clusters (2003)
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)
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)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Lezzi, D., Rafanell, R., Carrión, A., Espert, I.B., Hernández, V., Badia, R.M. (2012). Enabling e-Science Applications on the Cloud with COMPSs. In: Alexander, M., et al. Euro-Par 2011: Parallel Processing Workshops. Euro-Par 2011. Lecture Notes in Computer Science, vol 7155. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29737-3_4
Download citation
DOI: https://doi.org/10.1007/978-3-642-29737-3_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-29736-6
Online ISBN: 978-3-642-29737-3
eBook Packages: Computer ScienceComputer Science (R0)