Advertisement

An Interoperable GridWorkflow Management System

  • Maria Mirto
  • Marco Passante
  • Italo Epicoco
  • Giovanni Aloisio
Conference paper

Abstract

A WorkFlow Management System (WFMS) is a fundamental componentenabling to integrate data, applications and a wide set of project resources. Although a number of scientific WFMSs support this task, many analysis pipelines require large-scale Grid computing infrastructures to cope with their high compute and storage requirements. Such scientific workflows complicate the management of resources, especially in cases where they are offered by several resource providers, managed by different Grid middleware, since resource access must be synchronised in advance to allow reliable workflow execution. Different types of Grid middleware such as gLite, Unicore and Globus are used around the world and may cause interoperability issues if applications involve two or more of them. In this paperwe describe the ProGenGrid Workflow Management System which the main goal is to provide interoperability among these different grid middleware when executing workflows. It allows the composition of batch; parameter sweep and MPI based jobs. The ProGenGrid engine implements the logic to execute such jobs by using a standard language OGF compliant such as JSDL that has been extended for this purpose. Currently, we are testing our system on some bioinformatics case studies in the International Laboratory of Bioinformatics (LIBI) Project (www.libi.it).

Keywords

Grid Resource Parameter Sweep Bayesian Phylogenetic Inference Grid Portal Open Grid Forum 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    The NorduGrid web page. Http://www.nordugrid.org/
  2. 2.
    Alef, M., Fieseler, T., Freitag, S., Garcia, A., Grimm, C., Grich, W., Mehammed, H., Schley, L., Schneider, O., Volpato, G.: Integration of multiple middlewares on a single computing resource. Future Gener. Comput. Syst. 25(3), 268–274 (2009)CrossRefGoogle Scholar
  3. 3.
    Alfieri, R., Cecchini, R., Ciaschini, V., dellAgnello, L., Frohner, A., Lorentey, K., Spataro, F.From gridmap-file to VOMS: Managing authorization in a Grid environment. Future Gener. Comput. Syst. 21(4), 549–558 (2005)CrossRefGoogle Scholar
  4. 4.
    Almond, J., Snelling, D.: UNICORE: uniform access to supercomputing as an element of electronic commerce. Future Generation Computer Systems 15(5–6), 539–548 (1999)CrossRefGoogle Scholar
  5. 5.
    Aloisio, G., Cafaro, M., Carteni, G., Epicoco, I., Fiore, S., Lezzi, D., Mirto,M.,Mocavero, S.The Grid Resource Broker Portal. Concurrency and Computation: Practice and Experience, Special Issue on Grid Computing Environments 19(12), 1663–1670 (2007)CrossRefGoogle Scholar
  6. 6.
    Aloisio, G., Cafaro, M., Epicoco, I., Lezzi, D.: The GSI plug-in for gSOAP: Enhanced Security, Performance, and Reliability. In: Proceedings of Information Technology Coding and Computing (ITCC 2005), IEEE Press, pp. 304–309 (2005)Google Scholar
  7. 7.
    Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D.: Basic local alignment search tool. NucleicAcids Res. 3(215), 403–410 (1990). Http://www.ncbi.nlm.nih.gov/BLAST/ Google Scholar
  8. 8.
    Anjomshoaa, A., Brisard, F., Drescher, M., Fellows, D., Ly, A., McGough, S., Pulsipher, D., Savva, A.: Job submission description language (JSDL) specification, Version 1.0, Tech. Rep. GFD-R.056, Open Grid Forum, 2005 (2005). Http://forge.gridforum.org/projects/jsdl-wg
  9. 9.
    DEISA: Distributed European Infrastructure for Supercomputing Applications. Http://www.deisa.org/
  10. 10.
    Delaittre, T., Kiss, T., Goyeneche, A., Terstyanszky, G., Winter, S., Kacsuk, P.: GEMLCA: Running legacy code applications as grid services. Journal of Grid Computing 3(1–2), 7590 (2005)Google Scholar
  11. 11.
    Edgar, R.: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1), 113 (2004).CrossRefGoogle Scholar
  12. 12.
    EGEE: Enabling Grids for e-Science. Http://www.eu-egee.org/
  13. 13.
    Engelen, R.V., Gallivan, K.: The gSOAP Toolkit for Web Services and Peer-To-Peer Computing Networks. In: Proceedings of IEEE CCGrid Conference, pp. 128–135 (2002)Google Scholar
  14. 14.
    Foster, I., Kesselman, C.: Globus: A Metacomputing Infrastructure Toolkit. Intl J. Supercomputer Applications 11(2), 115–128 (1997)CrossRefGoogle Scholar
  15. 15.
    Foster, I., Kesselman, C., Tuecke, S.: The Anatomy of the Grid: Enabling Scalable Virtual Organizations. International Journal of High Performance Computing Applications 15(3), 200–222 (2001)CrossRefGoogle Scholar
  16. 16.
    Gjermundrod, H., Dikaiakos,M., Stumpert, M.,Wolniewicz, P., Kornmayer, H.: g-Eclipse an integrated framework to access and maintain Grid resources. In: 9th IEEE/ACM International Conference on Grid Computing, pp. 57–64 (2008)Google Scholar
  17. 17.
    Huedo, E., Montero, R., Llorente, I.: A framework for adaptive execution on grids. Internat. J. SoftwarePractice Experience (SPE) 34(7), 631–651 (2004)CrossRefGoogle Scholar
  18. 18.
    Kacsuk, P., Kiss, T., Sipos, G.: Solving the grid interoperability problem by P-GRADE portal at workflow level. Future Generation Computer Systems 24(7), 744–751 (2008)CrossRefGoogle Scholar
  19. 19.
    Kacsuk, P., Sipos, G.: Multi-Grid, Multi-User Workflows in the P-GRADE Grid Portal. Journal of Grid Computing 3(3–4), 221–238 (2005)Google Scholar
  20. 20.
    Krabbenhft, H., Mller, S., Bayer, D.: Integrating ARC Grid Middleware with Taverna Workflows. Bioinformatics 24(9), 1221–1222 (2008)CrossRefGoogle Scholar
  21. 21.
    Laure, E., Fisher, S., Frohner, A.: Programming the Grid with gLite. Computational Methods in Science and Technology 12(1), 33–45 (2006)Google Scholar
  22. 22.
    Maheshwari, K., Montagnat, J., Missier, P.: Extending taverna to exploit egee grid resources. In: e-science (2008)Google Scholar
  23. 23.
    Mirto, M., Cafaro, M., Epicoco, I., Aloisio, G.: Advances in the ProGenGrid Workflow Management System. In: IEEE Proceedings of the 1st International Workshop on High Performance Data Grid (HPDataGrid’08), held in conjunction with the 9th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT08), pp. 538–543 (2008)Google Scholar
  24. 24.
    Mirto, M., Vicario, S., Tartarini, D., Epicoco, I., Saccone, C., Aloisio, G.: Bayesian Phylogenetic Inference in the LIBI Grid platform: a tool to explore large data sets. In: IEEE Proceedings of the International Symposium on Parallel and Distributed Processing and Applications (ISPA 2008), pp. 855–860 (2008)Google Scholar
  25. 25.
    NGS: The UK National Grid Service Website. Http://www.ngs.ac.uk/
  26. 26.
    Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M., Wipat, A., Li, P. Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20(17), 3045–3054 (2004)CrossRefGoogle Scholar
  27. 27.
    Ronquist, F., Huelsenbeck, J.P.: MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 (2003)CrossRefGoogle Scholar
  28. 28.
    Taylor, I., Shields, M.,Wang, I., Harrison, A.: The Triana workflow environment: architecture and applications. In: In I. Taylor et al., editors, Workflows for e-Science, Springer-Verlag, pp.320–339 (2007)Google Scholar
  29. 29.
    The LIBI Grid Platform Developers, I.: Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare, chap. 29, pp. 577–613. Mario Cannataro, University Magna Graecia of Catanzaro, Italy, Medical Information Science Reference, IGI Global (2009)Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Maria Mirto
    • 1
  • Marco Passante
    • 1
  • Italo Epicoco
    • 1
  • Giovanni Aloisio
    • 1
  1. 1.University of SalentoSalentoItaly

Personalised recommendations