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Computing, Networking, Storage and Analysis
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SCHEDULE: NOV 15-20, 2015

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Parallel Distributed Memory Construction of Suffix and Longest Common Prefix Arrays

SESSION: Applications: Biophysics and Genomics

EVENT TYPE: Papers, Best Student Paper Finalists

TIME: 2:30PM - 3:00PM

SESSION CHAIR(S): Amanda Randles

AUTHOR(S):Patrick Flick, Srinivas Aluru



Suffix arrays and trees are fundamental string data structures of importance to
many applications in computational biology. Consequently, their parallel
construction is an actively studied problem. To date, algorithms with best
practical performance lack efficient worst-case run-time guarantees, and vice
versa. In addition, much of the recent work targeted low core count, shared
memory parallelization. In this paper, we present parallel algorithms for
distributed memory construction of suffix arrays and longest common prefix (LCP)
arrays that simultaneously achieve good worst-case run-time bounds and superior
practical performance. Our algorithms run in O(T_sort(n,p)log(n)) worst-case
time where T_sort(n,p) is the run-time of parallel sorting. We present
several algorithm engineering techniques that improve performance in practice.
We demonstrate the constructions of suffix and LCP arrays of the human genome in
less than 8 seconds on 1,024 Intel Xeon cores, reaching speedups of over 110X
compared to the best sequential suffix array construction implementation

Chair/Author Details:

Amanda Randles (Chair) - Duke University|

Patrick Flick - Georgia Institute of Technology

Srinivas Aluru - Georgia Institute of Technology

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Paper provided by the ACM Digital Library

Paper also available from IEEE Computer Society