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Exploring modern FPGA platforms for faster phylogeny reconstruction with RAxML

Malakonakis Pavlos, Brokalakis Andreas, Alachiotis Nikolaos, Sotiriadis Evripidis, Dollas Apostolos

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URIhttp://purl.tuc.gr/dl/dias/0FD55AC1-C9E0-4548-AC2A-7DBE50C763CC-
Identifierhttps://doi.org/10.1109/BIBE50027.2020.00024-
Identifierhttps://ieeexplore.ieee.org/document/9288011-
Languageen-
Extent8 pagesen
TitleExploring modern FPGA platforms for faster phylogeny reconstruction with RAxMLen
CreatorMalakonakis Pavlosen
CreatorΜαλακωνακης Παυλοςel
CreatorBrokalakis Andreasen
CreatorΜπροκαλακης Ανδρεαςel
CreatorAlachiotis Nikolaosen
CreatorΑλαχιωτης Νικολαοςel
CreatorSotiriadis Evripidisen
CreatorΣωτηριαδης Ευριπιδηςel
CreatorDollas Apostolosen
CreatorΔολλας Αποστολοςel
PublisherInstitute of Electrical and Electronics Engineersen
Content SummaryThe 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.en
Type of ItemΔημοσίευση σε Συνέδριοel
Type of ItemConference Publicationen
Licensehttp://creativecommons.org/licenses/by/4.0/en
Date of Item2022-01-07-
Date of Publication2020-
SubjectPhylogenetic inferenceen
SubjectPhylogenetic treeen
SubjectRAxML (Randomized Axelerated Maximum Likelihood)en
SubjectPLF (Phylogenetic Likelihood Function) en
SubjectPhylogenetic likelihooden
SubjectFPGA (Field Programmable Gate Array)en
SubjectReconfigurable hardwareen
SubjectAmazon AWS F1en
Bibliographic CitationP. Malakonakis, A. Brokalakis, N. Alachiotis, E. Sotiriades and A. Dollas, "Exploring modern FPGA platforms for faster phylogeny reconstruction with RAxML," in BIBE 2020, pp. 97-104, doi: 10.1109/BIBE50027.2020.00024en

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