Transformation of Suffix Arrays into Suffix Trees on the MPI Environment

Authors:
Inbok Lee;Costas S. Iliopoulos;Syng-Yup Ohn
Affiliations:
School of Electronics, Telecommunication, and Computer Engineering, Hankuk Aviation University,;King's College London, Department of Computer Science, London WC2R 2LS, UK;School of Electronics, Telecommunication, and Computer Engineering, Hankuk Aviation University,
Venue:
RSFDGrC '07 Proceedings of the 11th International Conference on Rough Sets, Fuzzy Sets, Data Mining and Granular Computing
Year:
2009

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Abstract

Suffix trees and suffix arrays are two well-known index data structures for strings. It is known that the latter can be easily transformed into the former: Iliopoulos and Rytter [5] showed two simple transformation algorithms on the CREW PRAM model. However, the PRAM model is a theoretical one and we need a practical parallel model. The Message Passing Interface (MPI) is a standard widely used on both massively parallel machines and on clusters.In this paper, we show how to implement the algorithms of Iliopoulos and Rytter on the MPI environment. Our contribution includes the modification of algorithms due to the lack of shared memory, small number of processors, communication costs between processors.