Thread scaling in Bioinformatics

Our work on improving thread-scaling in Bowtie, Bowtie 2 and HISAT appeared in Bioinformatics: While work on efficient genomics software has generally focused on speed on a fixed, small number of threads, general-purpose processors are now capable of running hundreds of threads of execution simultaneously in parallel. Intel’s Xeon Phi Knights Landing architecture for example supports 256–288 simultaneous threads. The underlying architectures are also complex; a many-core processor more resembles a small computer cluster on a chip than the Pentium chips of the past. Methods used to maximize efficiency on older processors are not well suited and more work is needed to enable genomics tools to exploit these architectures.

Here we tackled these issues, concentrating on the Bowtie, Bowtie 2 and HISAT tools since they are widely used and representative of a wider group of embarrassingly parallel tools. We explored key issues posed by these architectures and suggest solutions and measure their effect on thread scaling. We achieved great scaling to hundreds of threads, and this manuscript announces the availability of the new official releases of Bowtie and Bowtie 2 tools that implement these ideas. We also suggest a change to common genomics file formats, e.g. FASTA and FASTQ, that can yield substantial additional thread scaling benefits.

This work is supported by funds for the Intel Parallel Computing Center at Johns Hopkins University, NIH/NIGMS grant R01GM118568, and the Stampede 2 resource at the Texas Advanced Computing Center (TACC) that we accessed through XSEDE research project TG-CIE170020.


Published:July 18, 2018


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