Generating Parallel Algorithms for Cluster and Grid Computing

Abstract

We revisit and use the dependence transformation method to generate parallel algorithms suitable for cluster and grid computing. We illustrate this method in two applications: to obtain a systolic matrix product algorithm, and to compute the alignment score of two strings. The product of two n × n matrices is viewed as multiplying two p × p matrices whose elements are n/p × n/p submatrices. For m such multiplications, using p processors, the proposed parallel solution gives a linear speedup of mp 3 (m+2)p−2 or roughly p. The alignment problem of two strings of lengths m and n is solved in O(p) communication rounds and O(mn/p) local computing time. We show promising experimental results obtained on a 16-node Beowulf cluster and on an 18-node grid called InteGrade, consisting of desktop computers.

DOI: 10.1007/11428831_63

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Cite this paper

@inproceedings{Hayashida2005GeneratingPA, title={Generating Parallel Algorithms for Cluster and Grid Computing}, author={Ulisses Kendi Hayashida and Kunio Okuda and Jairo Panetta and Siang Wun Song}, booktitle={International Conference on Computational Science}, year={2005} }