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2013 Proceedings of the Fifteenth Workshop on Algorithm Engineering and Experiments (ALENEX)

Inducing Suffix and LCP Arrays in External Memory

Abstract

We consider text index construction in external memory (EM). Our first contribution is an inducing algorithm for suffix arrays in external memory. Practical tests show that this outperforms the previous best EM suffix sorter [Dementiev et al., ALENEX 2005] by a factor of about two in time and I/O-volume. Our second contribution is to augment the first algorithm to also construct the array of longest common prefixes (LCPs). This yields the first EM construction algorithm for LCP arrays. The overhead in time and I/O volume for this extended algorithm over plain suffix array construction is roughly two. Our algorithms scale far beyond problem sizes previously considered in the literature (text size of 80 GiB using only 4 GiB of RAM in our experiments).

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cover image Proceedings
2013 Proceedings of the Fifteenth Workshop on Algorithm Engineering and Experiments (ALENEX)
Pages: 88 - 102
Editors: Peter Sanders, Karlsruhe Institute of Technology, Karlsruhe, Germany and Norbert Zeh, Dalhousie University, Halifax, Nova Scotia, Canada
ISBN (Print): 978-1-611972-53-5
ISBN (Online): 978-1-61197-293-1

History

Published online: 18 December 2013

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*
Supported by DFG SPP 1307.
Supported by the German Research Foundation (DFG).
Partially supported by EU Project No. 248481 (PEPPHER) ICT-2009.3.6

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