A PGAS-Based Algorithm for the Longest Common Subsequence Problem

Authors:
M. Bakhouya;O. Serres;T. El-Ghazawi
Affiliations:
High Performance Computing Laboratory, George Washington University,;High Performance Computing Laboratory, George Washington University,;High Performance Computing Laboratory, George Washington University,
Venue:
Euro-Par '08 Proceedings of the 14th international Euro-Par conference on Parallel Processing
Year:
2008

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Abstract

Finding the Longest Common Subsequence (LCS) is a traditional and well studied problem in bioinformatics and text editing. In this paper, a customized parallel algorithm based on the Partitioned Global Address Space (PGAS) programming model to compute the LCS is presented. The algorithm is based on two related parameters balancing the communication and the synchronization needs in order to find the best data and workload distributions. The basic design of the algorithm and its complexity analysis are discussed together with experimental results. These results show the impact of those parameters on PGAS algorithm performance.