Parallel construction of wavelet trees on multicore architectures
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Parallel construction of wavelet trees on multicore architecturesDate
2016-10-05Citation
Fuentes-Sepúlveda, J., Elejalde, E., Ferres, L. et al. Knowl Inf Syst (2016). doi:10.1007/s10115-016-1000-6
Abstract
[Abstract] The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their construction time. In this paper, we introduce two algorithms that reduce the time complexity of a wavelet tree’s construction by taking advantage of nowadays ubiquitous multicore machines. Our first algorithm constructs all the levels of the wavelet in parallel with O(n) time and O(nlgσ+σlgn)O(nlgσ+σlgn) bits of working space, where n is the size of the input sequence and σσ is the size of the alphabet. Our second algorithm constructs the wavelet tree in a domain decomposition fashion, using our first algorithm in each segment, reaching O(lgn)O(lgn) time and O(nlgσ+pσlgn/lgσ)O(nlgσ+pσlgn/lgσ) bits of extra space, where p is the number of available cores. Both algorithms are practical and report good speedup for large real datasets.
Keywords
Succinct data structure
Wavelet tree construction
Multicore
Parallel algorithm
Wavelet tree construction
Multicore
Parallel algorithm
Description
The final publication is available at Springer via http://dx.doi.org/10.1007/s10115-016-1000-6
Editor version
ISSN
0219-1377
0219-3116
0219-3116