extended-abstract

Truly parallel burrows-wheeler compression and decompression

Authors:

James Alexander Edwards,

Uzi VishkinAuthors Info & Claims

SPAA '13: Proceedings of the twenty-fifth annual ACM symposium on Parallelism in algorithms and architectures

Pages 93 - 96

https://doi.org/10.1145/2486159.2486164

Published: 23 July 2013 Publication History

Abstract

We present novel work-optimal PRAM algorithms for Burrows-Wheeler (BW) compression and decompression of strings over a constant alphabet. For a string of length n, the depth of the compression algorithm is O(log² n), and the depth of the corresponding decompression algorithm is O(log n). These appear to be the first polylogarithmic-time work-optimal parallel algorithms for any standard lossless compression scheme.

The algorithms for the individual stages of compression and decompression may also be of independent interest: 1. a novel O(log n)-time, O(n)-work PRAM algorithm for Huffman decoding; 2. original insights into the stages of the BW compression and decompression problems, bringing out parallelism that was not readily apparent. We then mapped such parallelism in interesting ways to elementary parallel routines that have O(log n)-time, O(n)-work solutions, such as: (i) prefix-sums problems with an appropriately-defined associative binary operator for several stages, and (ii) list ranking for the final stage of decompression (inverse blocksorting transform).

Companion work reports empirical speedups of up to 25x for compression and up to 13x for decompression. This reflects a speedup of 70x over recent work on BW compression on GPUs.

References

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R. Cole and U. Vishkin. Deterministic coin tossing with applications to optimal parallel list ranking. Inf. Control, 70(1):32--53, July 1986.

Digital Library

[3]

R. Cole and U. Vishkin. Faster optimal parallel prefix sums and list ranking. Information and Computation, 81(3):334--352, 1989.

Digital Library

[4]

J. A. Edwards and U. Vishkin. Parallel algorithms for Burrows-Wheeler compression and decompression. TR, UMD, 2012. http://hdl.handle.net/1903/13299.

[5]

J. A. Edwards and U. Vishkin. Empirical speedup study of truly parallel data compression. TR, UMD, 2013. http://hdl.handle.net/1903/13890.

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A. Eirola. Lossless data compression on GPGPU architectures. ArXiv e-prints, 2011.

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J. Gilchrist and A. Cuhadar. Parallel lossless data compression based on the Burrows-Wheeler transform. Proc. Advanced Information Networking and Applications, 877--884, May 2007.

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J. Kärkkäainen, P. Sanders, and S. Burkhardt. Linear work suffix array construction. J. ACM, 53(6):918--936, Nov. 2006.

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S. T. Klein and Y. Wiseman. Parallel Huffman decoding with applications to JPEG files. The Computer Journal, 46(5):487--497, 2003.

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S. Lewin-Berlin. A parallel bzip2. http://software.intel.com/en-us/articles/a-parallel-bzip2, 2010.

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G. Nong, S. Zhang, and W. H. Chan. Linear suffix array construction by almost pure induced-sorting. Proc. Data Compression Conference, 193--202, 2009.

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R. Patel, Y. Zhang, J. Mak, A. Davidson, and J. Owens. Parallel lossless data compression on the GPU. Proc. Innovative Parallel Computing, 1--9, 2012.

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S. C. Sahinalp and U. Vishkin. Symmetry breaking for suffix tree construction. Proc. STOC'94, 300--309.

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J. Seward. bzip2, a program and library for data compression. http://www.bzip.org/.

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J. Seward. On the performance of BWT sorting algorithms. Proc. Data Compression Conference, 173--182, 2000.

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R. E. Tarjan and U. Vishkin. Finding biconnected components and computing tree functions in logarithmic parallel time. Proc. FOCS'84, 12--20.

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Cited By

Weißenberger ASchmidt B(2024)Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUsProceedings of the 53rd International Conference on Parallel Processing10.1145/3673038.3673067(856-865)Online publication date: 12-Aug-2024
https://dl.acm.org/doi/10.1145/3673038.3673067
Ghanim FVishkin UBarua R(2018)Easy PRAM-Based High-Performance Parallel Programming with ICEIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2017.275437629:2(377-390)Online publication date: 1-Feb-2018
https://doi.org/10.1109/TPDS.2017.2754376
Deshpande ANarayanan P(2015)Fast Burrows Wheeler Compression Using All-CoresProceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium Workshop10.1109/IPDPSW.2015.53(628-636)Online publication date: 25-May-2015
https://dl.acm.org/doi/10.1109/IPDPSW.2015.53

Index Terms

Truly parallel burrows-wheeler compression and decompression
1. Computing methodologies
  1. Parallel computing methodologies
    1. Parallel programming languages
2. Software and its engineering
  1. Software notations and tools
    1. General programming languages
      1. Language types
        Parallel programming languages

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cover image ACM Conferences

SPAA '13: Proceedings of the twenty-fifth annual ACM symposium on Parallelism in algorithms and architectures

July 2013

348 pages

ISBN:9781450315722

DOI:10.1145/2486159

General Chair:
Guy Blelloch
Carnegie Mellon University, USA
,
Program Chair:
Berthold Vöcking
RWTH Aachen University, Germany

Copyright © 2013 ACM.

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Published: 23 July 2013

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July 23 - 25, 2013

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Cited By

Weißenberger ASchmidt B(2024)Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUsProceedings of the 53rd International Conference on Parallel Processing10.1145/3673038.3673067(856-865)Online publication date: 12-Aug-2024
https://dl.acm.org/doi/10.1145/3673038.3673067
Ghanim FVishkin UBarua R(2018)Easy PRAM-Based High-Performance Parallel Programming with ICEIEEE Transactions on Parallel and Distributed Systems10.1109/TPDS.2017.275437629:2(377-390)Online publication date: 1-Feb-2018
https://doi.org/10.1109/TPDS.2017.2754376
Deshpande ANarayanan P(2015)Fast Burrows Wheeler Compression Using All-CoresProceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium Workshop10.1109/IPDPSW.2015.53(628-636)Online publication date: 25-May-2015
https://dl.acm.org/doi/10.1109/IPDPSW.2015.53

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