RAM-Efficient External Memory Sorting

In recent years a large number of problems have been considered in external memory models of computation, where the complexity measure is the number of blocks of data that are moved between slow external memory and fast internal memory (also called I/Os). In practice, however, internal memory time often dominates the total running time once I/O-efficiency has been obtained. In this paper we study algorithms for fundamental problems that are simultaneously I/O-efficient and internal memory efficient in the RAM model of computation.Comment: To appear in Proceedings of ISAAC 2013, getting the Best Paper Awar

Bidirectional Text Compression in External Memory

Bidirectional compression algorithms work by substituting repeated substrings by references that, unlike in the famous LZ77-scheme, can point to either direction. We present such an algorithm that is particularly suited for an external memory implementation. We evaluate it experimentally on large data sets of size up to 128 GiB (using only 16 GiB of RAM) and show that it is significantly faster than all known LZ77 compressors, while producing a roughly similar number of factors. We also introduce an external memory decompressor for texts compressed with any uni- or bidirectional compression scheme

Lempel-Ziv Parsing in External Memory

For decades, computing the LZ factorization (or LZ77 parsing) of a string has been a requisite and computationally intensive step in many diverse applications, including text indexing and data compression. Many algorithms for LZ77 parsing have been discovered over the years; however, despite the increasing need to apply LZ77 to massive data sets, no algorithm to date scales to inputs that exceed the size of internal memory. In this paper we describe the first algorithm for computing the LZ77 parsing in external memory. Our algorithm is fast in practice and will allow the next generation of text indexes to be realised for massive strings and string collections.Comment: 10 page

A Bulk-Parallel Priority Queue in External Memory with STXXL

We propose the design and an implementation of a bulk-parallel external memory priority queue to take advantage of both shared-memory parallelism and high external memory transfer speeds to parallel disks. To achieve higher performance by decoupling item insertions and extractions, we offer two parallelization interfaces: one using "bulk" sequences, the other by defining "limit" items. In the design, we discuss how to parallelize insertions using multiple heaps, and how to calculate a dynamic prediction sequence to prefetch blocks and apply parallel multiway merge for extraction. Our experimental results show that in the selected benchmarks the priority queue reaches 75% of the full parallel I/O bandwidth of rotational disks and and 65% of SSDs, or the speed of sorting in external memory when bounded by computation.Comment: extended version of SEA'15 conference pape