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Accelerating phylogenetics using FPGAs in the cloud

Alachiotis Nikolaos, Brokalakis Andreas, Amourgianos-Lorentzos Vasileios, Ioannidis Sotirios, Malakonakis Pavlos, Bokalidis Anastasios

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URIhttp://purl.tuc.gr/dl/dias/D0548287-BD72-4A1B-A12F-40FE85519E32-
Identifierhttps://doi.org/10.1109/MM.2021.3075848-
Identifierhttps://ieeexplore.ieee.org/document/9416903-
Languageen-
Extent7 pagesen
TitleAccelerating phylogenetics using FPGAs in the clouden
CreatorAlachiotis Nikolaosen
CreatorBrokalakis Andreasen
CreatorΜπροκαλακης Ανδρεαςel
CreatorAmourgianos-Lorentzos Vasileiosen
CreatorΑμουργιανος-Λορεντζος Βασιλειοςel
CreatorIoannidis Sotiriosen
CreatorΙωαννιδης Σωτηριοςel
CreatorMalakonakis Pavlosen
CreatorΜαλακωνακης Παυλοςel
CreatorBokalidis Anastasiosen
CreatorΜποκαλιδης Αναστασιοςel
PublisherInstitute of Electrical and Electronics Engineersen
Content SummaryPhylogenetics study the evolutionary history of organisms using an iterative process of creating and evaluating phylogenetic trees. This process is very computationally intensive; constructing a large phylogenetic tree requires hundreds to thousands of CPU hours. In this article, we describe an FPGA-based system that can be deployed on AWS EC2 F1 cloud instances to accelerate phylogenetic analyses by boosting performance of the phylogenetic likelihood function, i.e., a widely employed tree-evaluation function that accounts for up to 95% of the overall analysis time. We exploit domain-specific knowledge to reduce the amount of transferred data that limits overall system performance. Our proof-of-concept implementation reveals that the effective accelerator throughput nearly quadruples with optimized data movement, reaching up to 75% of its theoretical peak and nearly 10× faster processing than a CPU using AVX2 extensions.en
Type of ItemPeer-Reviewed Journal Publicationen
Type of ItemΔημοσίευση σε Περιοδικό με Κριτέςel
Licensehttp://creativecommons.org/licenses/by/4.0/en
Date of Item2022-11-01-
Date of Publication2021-
SubjectPhylogenyen
SubjectTopologyen
SubjectCentral Processing Uniten
SubjectMathematical modelen
SubjectProbabilityen
SubjectField programmable gate arraysen
Bibliographic CitationN. Alachiotis, A. Brokalakis, V. Amourgianos, S. Ioannidis, P. Malakonakis and T. Bokalidis, "Accelerating phylogenetics using FPGAs in the cloud," IEEE Micro, vol. 41, no. 4, pp. 24-30, 1 July-Aug. 2021, doi: 10.1109/MM.2021.3075848.en

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