SC21 Proceedings

The International Conference for High Performance Computing, Networking, Storage, and Analysis

Accelerating Large Scale de Novo Metagenome Assembly Using GPUs

Authors: Muaaz Gul Awan, Steven Hofmeyr, Rob Egan, Nan Ding, Aydin Buluc, Jack Deslippe, and Leonid Oliker (Lawrence Berkeley National Laboratory (LBNL)) and Katherine Yelick (University of California, Berkeley, Lawrence Berkeley National Laboratory (LBNL))

Abstract: Metagenomic workflows involve studying uncultured microorganisms directly from the environment. These environmental samples when processed by modern sequencing machines yield large and complex datasets which exceed the capabilities of metagenomic software. The increasing sizes and complexities of datasets make a strong case for exascale-capable metagenome assemblers. The underlying algorithmic motifs, however, are not well suited for GPUs. This poses a challenge since the majority of next generation supercomputers will rely primarily on GPUs for computation. In this paper we present the first of its kind GPU accelerated implementation of local assembly approach that is an integral part of a widely used large scale metagenome assembler, MetHipMer. Local assembly uses algorithms that induce random memory accesses and non-deterministic workloads, which make GPU offloading a challenging task. Our GPU implementation outperforms the CPU version by about 7x and boosts the performance of MetaHipMer by 42% when running on 64 Summit nodes.

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