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Fast and Lightweight Distributed Suffix Array Construction

Authors Manuel Haag , Florian Kurpicz , Peter Sanders , Matthias Schimek

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  • Theory of computation → Distributed algorithms
Keywords
  • Distributed Computing
  • Suffix Array Construction

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Abstract

The suffix array contains the lexicographical order of all suffixes of a text. It is one of the most well-studied text indices with applications in bioinformatics, compression, and pattern matching. The main bottleneck of distributed-memory suffix array construction algorithms is their memory requirements. Even careful implementations require 30×-60× the input size as working memory. We present a scalable and lightweight distributed-memory adaptation of the difference cover (DCX) suffix array construction algorithm. Our approach relies on novel bucketing and random chunk redistribution techniques which reduce our memory requirement to 20×-26× the input size for medium-sized inputs and to 14×-15× for large-sized inputs. Regarding running time, we achieve speedups of up to 5× over current state-of-the-art distributed suffix array construction algorithms.

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Manuel Haag, Florian Kurpicz, Peter Sanders, and Matthias Schimek. Fast and Lightweight Distributed Suffix Array Construction. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 47:1-47:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025) https://doi.org/10.4230/LIPIcs.ESA.2025.47

Author Details

Manuel Haag
  • Karlsruhe Institute of Technology, Germany
Florian Kurpicz
  • Karlsruhe Institute of Technology, Germany
Peter Sanders
  • Karlsruhe Institute of Technology, Germany
Matthias Schimek
  • Karlsruhe Institute of Technology, Germany

Funding

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 882500). The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time on the GCS Supercomputer SuperMUC-NG at Leibniz Supercomputing Centre (www.lrz.de). The authors gratefully acknowledge the computing time provided on the high-performance computer HoreKa by the National High-Performance Computing Center at KIT (NHR@KIT). This center is jointly supported by the Federal Ministry of Education and Research and the Ministry of Science, Research and the Arts of Baden-Württemberg, as part of the National High-Performance Computing (NHR) joint funding program (https://www.nhr-verein.de/en/our-partners). HoreKa is partly funded by the German Research Foundation (DFG).

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