Abstract
In this paper we present a parallel wavefront algorithm for computing an alignment between two strings A and C, with |A| = m and |C| = n. On a distributed memory parallel computer of p processors each with O((m + n)/p) memory, the proposed algorithm requires O(p) communication rounds and O(mn/p) local computing time. The novelty of this algorithm is based on a compromise between the workload of each processor and the number of communication rounds required, expressed by a parameter called α. The proposed algorithm is expressed in terms of this parameter that can be tuned to obtain the best overall parallel time in a given implementation. We show very promising experimental results obtained on a 64-node Beowulf machine. A characteristic of the wavefront communication requirement is that each processor communicates with few other processors. This makes it very suitable as a potential application for grid computing.
The second author was supported by CNPq, FINEP-PRONEX-SAI Proc. No. 76.97.1022.00 and FAPESP Proc. No. 1997/10982-0, the third author by the Natural Sciences and Engineering Research Council of Canada, and the fourth author by FAPESP Proc. No. 99/07390-0, CNPq Proc. No. 52.3778/96-1, 46.1230/00-3, 52.1097/01-0 and 52.2028/02-9.
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Alves, C.E.R., Cáceres, E.N., Dehne, F., Song, S.W. (2003). A Parallel Wavefront Algorithm for Efficient Biological Sequence Comparison. In: Kumar, V., Gavrilova, M.L., Tan, C.J.K., L’Ecuyer, P. (eds) Computational Science and Its Applications — ICCSA 2003. ICCSA 2003. Lecture Notes in Computer Science, vol 2668. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44843-8_27
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DOI: https://doi.org/10.1007/3-540-44843-8_27
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