Abstract
AbstractSuffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. We describe the first implementation and experimental evaluation of a scalable parallel algorithm for suffix array construction. The implementation works on distributed memory computers using MPI, Experiments with up to 128 processors show good constant factors and make it look likely that the algorithm would also scale to considerably larger systems. This makes it possible to build suffix arrays for huge inputs very quickly. Our algorithm is a parallelization of the linear time DC3 algorithm.KeywordsLoad ImbalanceSuffix ArrayArray ConstructionParallel SortingFull Text IndexThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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