Exploring Modern FPGA Platforms for Faster Phylogeny Reconstruction with RAxML

Pavlos Malakonakis, Andreas Brokalakis, Nikolaos Alachiotis, Evripides Sotiriades, Apostolos Dollas

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

Abstract

The Phylogenetic Likelihood Function (PLF) is one of the cornerstone functions in most phylogenetic inference tools; its execution represents the majority of time required to complete an analysis. This work proposes the acceleration of this function using reconfigurable hardware accelerators, focusing on system-on-chips that integrate Field Programmable Gate Array (FPGA) resources as well as traditional High Performance Computing (HPC) systems that use FPGA-based accelerator cards. Taking into account the specific properties of each platform in order to exploit their processing capabilities, the proposed solutions provide significant performance gains. The measured acceleration of PLF function is up to 8x while the overall time to complete a phylogenetic analysis using the popular RAxML software can be reduced up to 3.2 times (with respect to a pure software implementation on a high-end server processor). Compared to other similar solutions proposed in literature, our systems perform up to 65% faster.
Original languageEnglish
Title of host publication2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)
Place of PublicationPiscataway, NJ
PublisherIEEE
Number of pages8
ISBN (Electronic)978-1-7281-9574-2
ISBN (Print)978-1-7281-9575-9
DOIs
Publication statusPublished - 2020
Event20th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2020 - Cincinnati, United States
Duration: 26 Oct 202028 Oct 2020
Conference number: 20

Publication series

NameProceedings IEEE International Conference on Bioinformatics and Bioengineering (BIBE)
PublisherIEEE
Volume2020
ISSN (Print)2159-5410
ISSN (Electronic)2471-7819

Conference

Conference20th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2020
Abbreviated titleBIBE
CountryUnited States
CityCincinnati
Period26/10/2028/10/20

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