SC23 Proceedings

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

ACM Student Research Competition Poster Archive

Genome Assembly Using an Asynchronous Distributed Actor-Based Approach

Student: Souvadra Hati (Georgia Institute of Technology)
Supervisor: Richard Vuduc (Georgia Institute of Technology)

Abstract: We use genome assembly as a representative case to showcase the use of the ‘actor model’, a novel programming system for high-performance data-intensive workloads. The actor version of the 𝑘-mer counting kernel shows on average 1.6× speedup over similar MPI implementation. We provide a novel parallel algorithm that leverages the actor model to traverse de Bruijn graphs in a non-blocking, one-directional manner. Our findings highlight the potential of the actor model for writing simple and efficient parallel programs for data-heavy workloads.

ACM-SRC Semi-Finalist: no

Poster: PDF
Poster Summary: PDF

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