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Combining local and grid resources in scientific workflows (for Bioinformatics)
Linnaeus Centre for Bioinformatics, Uppsala Universitet.
Umeå University, Faculty of Science and Technology, Department of Computing Science. (UMIT)
Umeå University, Faculty of Science and Technology, Department of Computing Science.
Umeå University, Faculty of Science and Technology, Department of Computing Science.
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2009 (English)Conference paper, Published paper (Refereed)
Abstract [en]

We examine some issues that arise when using both local and Gridresources in scientific workflows. Our previous work addresses and illustratesthe benefits of a light-weight and generic workflow engine that manages andoptimizes Grid resource usage. Extending on this effort, we hereillustrate how a client tool for bioinformatics applications employs the engine tointerface with Grid resources. We also explore how to define data flowsthat transparently integrates local and Grid subworkflows. In addition, the benefits of parameter sweep workflows are examined and a means for describing this type of workflows in an abstract and concise manner is introduced. Finally, the above mechanisms are employed to perform an orthology detection analysis.

Place, publisher, year, edition, pages
Springer-Verlag , 2009.
Series
Lecture Notes in Computer Sciencce, ISSN 0302-9743 ; 6126, 6127
Keyword [en]
Grid, workflow, data flow, parameter sweep, bioinformatics
National Category
Computer Science
Research subject
Computing Science
Identifiers
URN: urn:nbn:se:umu:diva-19545OAI: oai:DiVA.org:umu-19545DiVA: diva2:202187
Conference
The 9th International Workshop on State-of-the-Art in Scientific and Parallel Computing, May 13-16 2008, NTNU, Trondheim, Norway
Note
accepted 2009Available from: 2009-03-09 Created: 2009-03-06 Last updated: 2012-08-15Bibliographically approved
In thesis
1. Portable Tools for Interoperable Grids: Modular Architectures and Software for Job and Workflow Management
Open this publication in new window or tab >>Portable Tools for Interoperable Grids: Modular Architectures and Software for Job and Workflow Management
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The emergence of Grid computing infrastructures enables researchers to shareresources and collaborate in more efficient ways than before, despite belongingto different organizations and being geographically distributed. While the Gridcomputing paradigm offers new opportunities, it also gives rise to newdifficulties. This thesis investigates methods, architectures, and algorithmsfor a range of topics in the area of Grid resource management. One studiedtopic is how to automate and improve resource selection, despite heterogeneityin Grid hardware, software, availability, ownership, and usage policies.Algorithmical difficulties for this are, e.g., characterization of jobs andresources, prediction of resource performance, and data placementconsiderations. Investigated Quality of Service aspects of resource selectioninclude how to guarantee job start and/or completion times as well as how tosynchronize multiple resources for coordinated use through coallocation.Another explored research topic is architectural considerations for frameworksthat simplify and automate submission, monitoring, and fault handling for largeamounts of jobs. This thesis also investigates suitable Grid interactionpatterns for scientific workflows, studies programming models that enable dataparallelism for such workflows, as well as analyzes how workflow compositiontools should be designed to increase flexibility and expressiveness. We today have the somewhat paradoxical situation where Grids, originally aimed tofederate resources and overcome interoperability problems between differentcomputing platforms, themselves struggle with interoperability problems causedby the wide range of interfaces, protocols, and data formats that are used indifferent environments. This thesis demonstrates how proof-of-concept softwaretools for Grid resource management can, by using (proposed) standard formatsand protocols as well as leveraging state-of-the-art principles fromservice-oriented architectures, be made independent of current Gridinfrastructures. Further interoperability contributions include an in-depthstudy that surveys issues related to the use of Grid resources in scientificworkflows. This study improves our understanding of interoperability amongscientific workflow systems by viewing this topic from three differentperspectives: model of computation, workflow language, and executionenvironment. A final contribution in this thesis is the investigation of how the design ofGrid middleware tools can adopt principles and concepts from softwareengineering in order to improve, e.g., adaptability and interoperability.

Place, publisher, year, edition, pages
Umeå: Umeå Universitet, Institutionen för Datavetenskap, 2009. 254 p.
Series
Report / UMINF, ISSN 0348-0542 ; 09.08
Keyword
Grid computing, scheduling, resource brokering, performance predictions, advance reservations, coallocation, standards-based infrastructure, interoperability, service-oriented architecture, job management, workflows, data flow
National Category
Computer Science
Identifiers
urn:nbn:se:umu:diva-19630 (URN)978-91-7264-754-1 (ISBN)
Public defence
2009-04-03, MA121, MIT-huset, SE 901 87, Umeå, 13:15 (English)
Opponent
Supervisors
Available from: 2009-03-13 Created: 2009-03-09 Last updated: 2009-03-13Bibliographically approved

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Citation style
  • apa
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  • Other style
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Language
  • de-DE
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  • Other locale
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Output format
  • html
  • text
  • asciidoc
  • rtf