Algorithms and data structures for external memory

Data sets in large applications are often too massive to fit completely inside the computer's internal memory. The resulting input/output communication (or I/O) between fast internal memory and slower external memory (such as disks) can be a major performance bottleneck. In this manuscript, we survey the state of the art in the design and analysis of algorithms and data structures for external memory (or EM for short), where the goal is to exploit locality and parallelism in order to reduce the I/O costs. We consider a variety of EM paradigms for solving batched and online problems efficiently in external memory.

For the batched problem of sorting and related problems like permuting and fast Fourier transform, the key paradigms include distribution and merging. The paradigm of disk striping offers an elegant way to use multiple disks in parallel. For sorting, however, disk striping can be nonoptimal with respect to I/O, so to gain further improvements we discuss distribution and merging techniques for using the disks independently. We also consider useful techniques for batched EM problems involving matrices, geometric data, and graphs.

In the online domain, canonical EM applications include dictionary lookup and range searching. The two important classes of indexed data structures are based upon extendible hashing and B-trees. The paradigms of filtering and bootstrapping provide convenient means in online data structures to make effective use of the data accessed from disk. We also re-examine some of the above EM problems in slightly different settings, such as when the data items are moving, when the data items are variable-length such as character strings, when the data structure is compressed to save space, or when the allocated amount of internal memory can change dynamically.

Programming tools and environments are available for simplifying the EM programming task. We report on some experiments in the domain of spatial databases using the TPIE system (Transparent Parallel I/O programming Environment). The newly developed EM algorithms and data structures that incorporate the paradigms we discuss are significantly faster than other methods used in practice.