Better External Memory LCP Array Construction

Abstract

The suffix array, perhaps the most important data structure in modern string processing, needs to be augmented with the longest-common-prefix (LCP) array in many applications. Their construction is often a major bottleneck, especially when the data is too big for internal memory. We describe two new algorithms for computing the LCP array from the suffix array in external memory. Experiments demonstrate that the new algorithms are about a factor of two faster than the fastest previous algorithm. We then further engineer the two new algorithms and improve them in three ways. First, we speed up the algorithms by up to a factor of two through parallelism. Eight threads is sufficient for making the algorithms essentially I/O bound. Second, we reduce the disk space usage of the algorithms making them in-place: the input (text and suffix array) is treated as read-only, and the working disk space never exceeds the size of the final output (the LCP array). Third, we add support for large alphabets. All previous implementations assume the byte alphabet.