Presentation
A Kokkos-Based Proxy of the Exascale Metagenome Assembler MetaHipMer2: A First Use of Kokkos for Computational Biology
DescriptionInexpensive DNA sequencing [1] has opened new windows into biological complexity. These include metagenomics: the ability to catalog a microbial ecosystem by extracting and sequencing DNA directly from an environment. Analyzing metagenomic-scale datasets often requires exascale computing. Such computing platforms are heterogeneous, encompassing CPUs, GPUs, FPGAs or other co-processors. This heterogeneity presents complications for software design. The programming models can require code rewrites when hardware changes. Moreover, achieving adequate performance requires understanding the interaction between hardware and programming models. Computational biology codes suffer particularly from these problems because they are poorly studied [2] [3]. Here we describe a proxy application based on a metagenome assembler which allows both machine profiling and studying co-processor behavior for biology codes.
Event Type
Research and ACM SRC Posters
TimeThursday, 20 November 20258:00am - 5:00pm CST
LocationSecond Floor Atrium
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