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Parallel Suffix Sorting for Large String Analytics

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Parallel Processing and Applied Mathematics (PPAM 2022)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 13826))

Abstract

The suffix array is a fundamental data structure to support string analysis efficiently. It took about 26 years for the sequential suffix array construction algorithm to achieve \(\mathcal {O}(n)\) time complexity and in-place sorting. In this paper, we develop the D-Limited Parallel Induce (DLPI) algorithm, the first \(\mathcal {O}(\frac{n}{p})\) time parallel suffix array construction algorithm. The basic idea of DLPI includes two aspects: dividing the \(\mathcal {O}(n)\) size problem into p reduced sub-problems with size \(\mathcal {O}(\frac{n}{p})\) so we can handle them on p processors in parallel; developing an efficient parallel induce sorting method to achieve correct order for all the reduced sub-problems. The complete algorithm description is given to show the implementation method of the proposed idea. The time and space complexity analysis and proof are also given to show the correctness and efficiency of the proposed algorithm. The proposed DLPI algorithm can handle large strings with scalable performance.

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Acknowledgement

This research was funded in part by NSF grant number CCF-2109988.

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Authors and Affiliations

  1. New Jersey Institute of Technology, Newark, NJ, USA

    Zhihui Du & David A. Bader

  2. State University of New York, College at Oneonta, Oneonta, NY, USA

    Sen Zhang

Authors
  1. Zhihui Du
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  2. Sen Zhang
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  3. David A. Bader
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Corresponding author

Correspondence to Zhihui Du .

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Editors and Affiliations

  1. Czestochowa University of Technology, Czestochowa, Poland

    Roman Wyrzykowski

  2. University of Tennessee, Knoxville, TN, USA

    Jack Dongarra

  3. University of Southern California, Marina del Rey, CA, USA

    Ewa Deelman

  4. Czestochowa University of Technology, Czestochowa, Poland

    Konrad Karczewski

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Du, Z., Zhang, S., Bader, D.A. (2023). Parallel Suffix Sorting for Large String Analytics. In: Wyrzykowski, R., Dongarra, J., Deelman, E., Karczewski, K. (eds) Parallel Processing and Applied Mathematics. PPAM 2022. Lecture Notes in Computer Science, vol 13826. Springer, Cham. https://doi.org/10.1007/978-3-031-30442-2_6

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  • DOI: https://doi.org/10.1007/978-3-031-30442-2_6

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-30441-5

  • Online ISBN: 978-3-031-30442-2

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