Fast Burrows Wheeler Compression Using All-Cores

Abstract

In this paper, we present an all-core implementation of Burrows Wheeler Compression algorithm that exploits all computing resources on a system. Our focus is to provide significant benefit to everyday users on common end-to-end applications by exploiting the parallelism of multiple CPU cores and additional accelerators, viz. Many-core GPU, on their machines. The all-core framework is suitable for problems that process large files or buffers in blocks. We consider a system to be made up of compute stations and use a work-queue to dynamically divide the tasks among them. Each compute station uses an implementation that optimally exploits its architecture. We develop a fast GPU BWC algorithm by extending the state-of-the-art GPU string sort to efficiently perform BWT step of BWC. Our hybrid BWC with GPU acceleration achieves a 2.9× speedup over best CPU implementation. Our all-core framework allows concurrent processing of blocks by both GPU and all available CPU cores. We achieve a 3.06× speedup by using all CPU cores and a 4.87× speedup when we additionally use an accelerator i.e. GPU. Our approach will scale to the number and different types of computing resources or accelerators found on a system.