Abstract
Sorting the suffixes of an input string is a fundamental task in many applications such as data compression, genome alignment, and full-text search. The induced sorting (IS) method has been successfully applied to design a number of state-of-the-art suffix sorting algorithms. In particular, the SAIS algorithm designed by the IS method is not only linear in time but also fast in practice. However, the parallelization of SAIS remains a challenge due to that the IS process in the algorithm is inherently sequential and the performance bottleneck of the whole algorithm. This article presents our attempt for designing a parallel variant of SAIS on a multicore machine which is considered as a shared memory parallel model, called pSAIS. By a combined use of multithreading and pipelining, the inducing process is accelerated by fully utilizing the machine’s parallel computing power. An experimental study is conducted for performance evaluation of pSAIS with the other existing parallel suffix sorting algorithms, on a set of realistic inputs with varying sizes and alphabets. The experiment results show that our program for pSAIS has a high degree of parallelism and achieves the best average time and space performance among all the parallel algorithms in comparison. While pSAIS is designed for quickly building big suffix arrays in a multicore machine, our study may give some hints for extending the induced sorting method to GPU for constructing small suffix arrays even faster.
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Notes
Both programs were downloaded from http://code.google.com/p/ge-nong/.
References
Arabnia HR, Oliver MA (1986) Fast operations on raster images with SIMD machine architectures. Comput Graph Forum 5(3):179–188
Burrows M, Wheeler DJ (1994) A block-sorting lossless data compression algorithm. SRC Res Rep 124:1–24
Ferragina P, Navarro G (2005) Pizza&Chili Corpus, compressed indexes and their testbeds. http://pizzachili.dcc.uchile.cl
Fischer J (2011) Inducing the LCP-array. In: Proceedings of the 12th International Symposium on Algorithms and Data Structures. Springer, pp 374–385
Intel Corporation (2017) Intel TBB, a widely used C++ template library for task parallelism. https://www.threadingbuildingblocks.org
Kärkkäinen J, Kempa D, Puglisi SJ, Zhukova B (2017) Engineering external memory induced suffix sorting. In: Proceedings of the 19th Workshop on Algorithm Engineering and Experiments. SIAM, pp 98–108
Labeit J, Shun J, Blelloch GE (2017) Parallel lightweight wavelet tree, suffix array and FM-index construction. J Discrete Algorithms 43(1):2–17
Liu WJ, Nong G, Chan WH, Wu Y (2016) Improving a lightweight LZ77 computation algorithm for running faster. Softw Pract Exp 46(9):1201–1217
Manber U, Myers G (1993) Suffix arrays: a new method for on-line string searches. SIAM J Comput 22(5):935–948
Michailidis PD, Margaritis KG (2016) Scientific computations on multi-core systems using different programming frameworks. Appl Numer Math 104:62–80
Mori Y (2010) sais-lite-2.4.1, an optimized implementation of the induced sorting algorithm. https://sites.google.com/site/yuta256/sais/
Mori Y (2015) Libdivsufsort, a software library that implements a lightweight suffix array construction algorithm. https://github.com/y-256/libdivsufsort
Nawaz MS, Lali MI, Saleem S, Ali H (2014) Comparison of multi-core parallel programming models for divide and conquer algorithms. NED University Journal of Research, pp 1–8
Nong G (2013) Practical linear-time O(1)-workspace suffix sorting for constant alphabets. ACM Trans Inf Syst 31(3):15:1–15:15
Nong G, Zhang S, Chan WH (2011) Two efficient algorithms for linear time suffix array construction. IEEE Trans Comput 60(10):1471–1484
Puglisi SJ, Smyth WF, Turpin AH (2007) A taxonomy of suffix array construction algorithms. ACM Comput Surv 39(2):4:1–4:31
Sanchez LM, Fernandez J, Sotomayor R, Escolar S, Garcia JD (2013) A comparative study and evaluation of parallel programming models for shared-memory parallel architectures. New Gener Comput 31(3):139–161
Shrestha AMS, Frith MC, Horton P (2014) A bioinformatician’s guide to the forefront of suffix array construction algorithms. Brief Bioinform 15(2):138–154
Shun J, Blelloch GE (2014) A simple parallel cartesian tree algorithm and its application to parallel suffix tree construction. ACM Trans Parallel Comput 1(1):8:1–8:20
Shun J, Blelloch GE, Fineman JT, Gibbons PB, Kyrola A, Simhadri HV, Tangwongsan K (2012) Brief announcement: the problem based benchmark suite. In: Proceedings of the Twenty-fourth Annual ACM Symposium on Parallelism in Algorithms and Architectures, ACM, pp 68–70
Valafar H, Arabnia HR, Williams G (2004) Distributed global optimization and its development on the multiring network. Neural Parallel Sci Comput 12(4):465–490
Wang L, Baxter S, Owens JD (2016) Fast parallel skew and prefix-doubling suffix array construction on the GPU. Concurr Comput Pract Exp 28(12):3466–3484
Wani MA, Arabnia HR (2003) Parallel edge-region-based segmentation algorithm targeted at reconfigurable multiring network. J Supercomput 25(1):43–62
Acknowledgements
The work of B. Lao was supported by the Guangzhou Science and Technology Program Grant No. 201707010165. The work of G. Nong was supported by the Guangdong Science and Technology Program Grant No. 2017A050506025. The work of W. H. Chan was supported by the General Research Fund (Grant No. 18300215) from the Research Grant Council of the University Grants Committee of Hong Kong SAR.
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Lao, B., Nong, G., Chan, W.H. et al. Fast induced sorting suffixes on a multicore machine. J Supercomput 74, 3468–3485 (2018). https://doi.org/10.1007/s11227-018-2395-5
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DOI: https://doi.org/10.1007/s11227-018-2395-5