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Scalable Parallel Suffix Array Construction

Kulla, Fabian; Sanders, Peter

Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. We describe the first implementation and experimental evaluation of a scalable parallel algorithm for suffix array construction. The implementation works on distributed memory computers using MPI, Experiments with up to 128 processors show good constant factors and make it look likely that the algorithm would also scale to considerably larger systems. This makes it possible to build suffix arrays for huge inputs very quickly. Our algorithm is a parallelization of the linear time DC3 algorithm.

DOI: 10.1007/11846802_12
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Proceedingsbeitrag
Publikationsjahr 2006
Sprache Englisch
Identifikator ISBN: 978-3-540-39112-8
ISSN: 0302-9743, 1611-3349
KITopen-ID: 1000097661
Erschienen in Recent Advances in Parallel Virtual Machine and Message Passing Interface. Ed.: B. Mohr
Verlag Springer Verlag
Seiten 22–29
Serie Lecture Notes in Computer Science ; 4192
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