A bridging model for parallel computation
Communications of the ACM
Efficient parallel algorithms for string editing and related problems
SIAM Journal on Computing
Fast text searching: allowing errors
Communications of the ACM
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Parallel dynamic programming for solving the string editing problem on a CGM/BSP
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A parallel BSP algorithm for irregular dynamic programming
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ICCSA'06 Proceedings of the 2006 international conference on Computational Science and Its Applications - Volume Part V
A tunable coarse-grained parallel algorithm for irregular dynamic programming applications
HiPC'04 Proceedings of the 11th international conference on High Performance Computing
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ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part I
Autotuning Wavefront Applications for Multicore Multi-GPU Hybrid Architectures
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Efficient Parallel Implementations of Multiple Sequence Alignment using BSP/CGM Model
Proceedings of Programming Models and Applications on Multicores and Manycores
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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.