Scalable Parallel Suffix Array Construction | Zendy

Fabian Kulla | Zendy; Peter Sanders | Zendy

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Scalable Parallel Suffix Array Construction

Author(s) -

Fabian Kulla,

Peter Sanders

Publication year - 2006

Publication title -

lecture notes in computer science

Language(s) - English

Resource type - Book series

SCImago Journal Rank - 0.249

H-Index - 400

eISSN - 1611-3349

pISSN - 0302-9743

DOI - 10.1007/11846802_12

Subject(s) - computer science , suffix array , scalability , parallel computing , suffix , programming language , data structure , database , linguistics , philosophy

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.

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