Abstract
Hierarchical grid computing is a way to gain high compute power at low cost by combining existing computational resources instead of building a new one. It typically has heterogeneous characteristics, such as: (1) Resources have different computational power; and (2) Resources are shared among users; and (3) Resources are usually connected by networks with widely varying performance characteristics. This makes the development or adaptation of parallel applications on hierarchical grids challenging. In this paper, we study three load balancing techniques for hierarchical grids: static load balancing, master-slave and a new technique called “scheduler-worker”. We evaluate the performance of these techniques for computing the alignment of long DNA sequences on a grid.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Chen, C.X., Schmidt, B.: Computing Large-scale Alignments on a Multi-cluster. In: Cluster 2003, Hongkong (2003)
Chen, C.X., Schmidt, B.: Performance Analysis of Computational Biology Applications on Hierarchical Grid Systems. In: CCGrid 2004, Chicago (2004)
Foster, I., Kesselman, C.: The Grid 2: Blueprint for a New Computing Infrastructure. Morgan Kaufmann, San Francisco (2004)
Gabriel, E., Resch, M., Beisel, T., Keller, R.: Distributed computing in a heterogeneous computing environment. In: Alexandrov, V.N., Dongarra, J. (eds.) PVM/MPI 1998. LNCS, vol. 1497, pp. 180–187. Springer, Heidelberg (1998)
Hirschberg, D.S.: A linear space algorithm for computing longest common subsequences. Comm. ACM 18, 341–343 (1975)
Huang, X., Miller, W.: A time efficient, linear-space local similarity algorithm. Advances in Applied Mathematics 12, 337–357 (1991)
Imamura, T., Tsujita, Y., Koide, H., Takemiya, H.: An architecture of Stampi: MPI library on a cluster of parallel computers. In: Dongarra, J., Kacsuk, P., Podhorszki, N. (eds.) PVM/MPI 2000. LNCS, vol. 1908, pp. 200–207. Springer, Heidelberg (2000)
Karonis, N.T., Toonen, B.: MPICH-G2 project: http://www3.niu.edu/mpi
Kielmann, T., Hofman, R.F.H., Bal, H.E., Plaat, A., Bhoedjang, R.A.F.: MagPIe: MPI’s collective communication operations for clustered wide area systems. In: Ppopp 1999, pp. 131–140. ACM, New York (1999)
Müller, M., Hess, M., Gaberel, E.: Grid enabled MPI solutions for Clusters. In: CCGrid 2003, Tokyo, Japan (2003)
Myers, E., Miller, W.: Optimal alignments in linear space. Computer Applications in the Biosciences 4, 11–17 (1988)
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. Journal of Molecular Biology 147, 195–197 (1981)
Stewart, C.A., Hart, D., Berry, D.K., Olsen, G.J., Wernert, E.A., Fischer, W.: Parallel implementation and performance of fastDNAml: a program for maximum likelihood phylogenetic inference. In: SC 2001, Denver, CO, USA (2001)
Waterman, M.S., Eggert, M.: A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. Journal of Molecular Biology 197, 723–728 (1987)
Zhu, W.R., Niu, Y.W., Lu, J.Z., Shen, C., Gao, G.R.: A Cluster-Based Solution for High Performance Hmmpfam Using EARTH Execution Model. In: Cluster 2003, Hongkong (2003)
GLOBUS project: http://www.globus.org
MPICH project: http://www-unix.mcs.anl.gov/mpi/mpich/
Sun grid engine project: http://gridengine.sunsource.net/
openPBS project: http://www.openpbs.org/
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Chen, C., Schmidt, B. (2004). Load Balancing for Hierarchical Grid Computing: A Case Study. In: Bougé, L., Prasanna, V.K. (eds) High Performance Computing - HiPC 2004. HiPC 2004. Lecture Notes in Computer Science, vol 3296. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30474-6_39
Download citation
DOI: https://doi.org/10.1007/978-3-540-30474-6_39
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-24129-4
Online ISBN: 978-3-540-30474-6
eBook Packages: Computer ScienceComputer Science (R0)