Engineering Lightweight Burrows-Wheeler Transform Construction on the GPU via Prefix-Free Parsing

Abstract

The Burrows-Wheeler transform (BWT) is the core of many compressed full-text indexes and most read aligners. The fastest BWT constructions on GPUs need about $20$ bytes of device memory per character, which severely limits the texts that can be processed there. For example, on our GPU with 24 GB device memory, this is only about 1200 MiB. Prefix-free parsing (PFP) can be used to reduce the memory requirements of BWT construction algorithms in main memory. But, it uses hash tables and inverted lists which are not suited for GPUs. We show that PFP-based BWT construction can work with only sorting, scanning, and simple data-parallel procedures. This results in our GPU construction gpupfpbwt that on an NVIDIA RTX 3090, reduces the peak memory on an English text 11.9 bytes per character. There, it can processes 2108 MiB input files, which is 1.8 times larger than what the current state of the art libcubwt can handle. It is faster than or on par with libcubwt on eight of nine repetitive texts but 2.0 to 3.2 times slower on five of six non-repetitive ones, i.e., it provides a trade-off between required device memory and throughput.