Scientific applications on GRID systems
Participants
- Sverker Holmgren (Professor in Scientific Computing)
- Mahen Jayawardena (Former PhD student. Principal advisor Prof. Sverker Holmgren )
- Salman Toor (PhD in Scientific Computing)
The group collaborates with
Cloud and Grid Computing Group
at Umeå University
Örjan Carlborg's group at the Swedish University of Agricultural Sciences (SLU)
Computational System Biology group at the Scientific Computing Division of Uppsala University
Research
Background: Distributed Computing Infrastructure (DCI) such as grids allow scientists to run their computational experiments to an extent that was not previously possible. Applications ranging from Astronomy, Medical Sciences, Image Analysis to Structural Mechanics are gaining huge benefits out of such infrastructures. By connecting geographically distributed resources, grids provides a variety of computational and storage resources to be available seamlessly. This technology allows to initiate large scale studies which helps to give more precise and in-depth details about the complex phenomena. One of the outstanding example is the use of grids in CERN's LHC (Large Hadron Collider) experiment where grid systems is the choice for processing and storing petascale of data. A number of middlewares (Software stack used to build grid infrastructure) with different set of components are running in several production ready environments, and most of them follows the Service Oriented Architecture (SAO), for example ARC (Advanced Resource Connector), gLite and Globus Toolkit. Due to the heterogeneous nature of the available resources, it still require a fair amount of work to port applications to a given grid system. Also there are a number of open research areas in building more reliable, efficient and easy-to-use grid systems.
Articles and Reviewed Conference Contributions
- J. K. Nilsen, S. Toor, Zs. Nagy, B. Mohn, and A. L. Read. Perfor- mance and Stability of the Chelonia Storage Cloud. Ready to be submitted.
- M. Jayawardena, C. Nettelblad, S. Toor, P-O. Östberg, E. Elmroth and S. Holmgren. A Grid-Enabled Problem Solving Environment for QTL Analysis in R. Accepted for publication in Proc. 2nd Interna- tional Conference on Bioinformatics and Computational Biology (BI- CoB 2010), 2010.
- J. K. Nilsen, S. Toor, Zs. Nagy and B. Mohn. Chelonia - A Self-healing Storage Cloud. In M. Bubak, M. Turala, and K. Wiatr, editors, CGW´09 Proceedings, Krakow, 2 2010. ACC CYFRONET AGH. ISBN 978-83-61433-01-9.
- S. Toor, B. Mohn, S. Holmgren. Case-Study for Different Models of Resource Brokering in Grid Systems. Technical Report no. 2010-009, Department of Information Technology, Uppsala University.
- Jon Kerr Nilsen, Salman Toor, Zsombor Nagy and Alex Read. Chelonia: A self-healing, replicated storage system. Submitted to the International Conference on Computing in High Energy and Nuclear Physics (CHEP) 2010.
- E. Elmroth, S. Holmgren, J. Lindemann, S. Toor, and P-O. Östberg. Empowering a Flexible Application Portal with a SOA-based Grid Job Management Framework. Accepted for publication in Proc. 9th Work- shop on State-of-the-art in Scientific and Parallel Computing (PARA 2008), Lecture Notes in Computer Science, Springer-Verlag.
- Grid-enabling an efficient algorithm for demanding global optimization problems in genetic analysis. Mahen Jayawardena and Sverker Holmgren. In Proc. 3rd International Conference on e-Science and Grid Computing, pp 205-212, IEEE, Piscataway, NJ, 2007.
Theses
- Parallel algorithms and implementations for genetic analysis of quantitative traits. Mahen Jayawardena. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2007-005, 2007. (Supervised by Prof. Sverker Holmgren )
- An e-Science Approach to Genetic Analysis of Quantitative Traits. Mahen Jayawardena. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 708, Acta Universitatis Upsaliensis, Uppsala, 2010. (Supervised by Prof. Sverker Holmgren )
- Managing applications and data in distributed computing infrastructures. Salman Toor. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2010-003, 2010. (Supervised by Prof. Sverker Holmgren )
Supervised M.Sc. Theses and Project Reports
- Salman Toor, A Grid Portal Implementation for Genetic Mapping of Multiple QTL. MSc Thesis in Scientific Computing, Uppsala University, 2007. (Supervised by Prof. Sverker Holmgren)
Software
Chelonia Storage, Developed with in the collaboration of NorduGrid.