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Scalable Parallel Suffix Array Construction

In: High Performance Computing in Science and Engineering ’06

Author

Listed:
  • Fabian Kulla

    (Forschungszentrum Karlsruhe)

  • Peter Sanders

    (Universität Karlsruhe)

Abstract

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.

Suggested Citation

  • Fabian Kulla & Peter Sanders, 2007. "Scalable Parallel Suffix Array Construction," Springer Books, in: Wolfgang E. Nagel & Willi Jäger & Michael Resch (ed.), High Performance Computing in Science and Engineering ’06, pages 543-546, Springer.
    • Handle: RePEc:spr:sprchp:978-3-540-36183-1_39
    DOI: 10.1007/978-3-540-36183-1_39
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