BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.
Bayesian phylogenetics
GPU
maximum likelihood
multicore processing
parallel computing
Journal
Systematic biology
ISSN: 1076-836X
Titre abrégé: Syst Biol
Pays: England
ID NLM: 9302532
Informations de publication
Date de publication:
01 11 2019
01 11 2019
Historique:
received:
27
04
2018
revised:
10
04
2019
accepted:
10
04
2019
pubmed:
30
4
2019
medline:
10
1
2020
entrez:
30
4
2019
Statut:
ppublish
Résumé
BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrated into recent versions of popular phylogenetics software packages including BEAST and MrBayes and has been widely used across a diverse range of evolutionary studies. Here, we present BEAGLE 3 with new parallel implementations, increased performance for challenging data sets, improved scalability, and better usability. We have added new OpenCL and central processing unit-threaded implementations to the library, allowing the effective utilization of a wider range of modern hardware. Further, we have extended the API and library to support concurrent computation of independent partial likelihood arrays, for increased performance of nucleotide-model analyses with greater flexibility of data partitioning. For better scalability and usability, we have improved how phylogenetic software packages use BEAGLE in multi-GPU (graphics processing unit) and cluster environments, and introduced an automated method to select the fastest device given the data set, evolutionary model, and hardware. For application developers who wish to integrate the library, we also have developed an online tutorial. To evaluate the effect of the improvements, we ran a variety of benchmarks on state-of-the-art hardware. For a partitioned exemplar analysis, we observe run-time performance improvements as high as 5.9-fold over our previous GPU implementation. BEAGLE 3 is free, open-source software licensed under the Lesser GPL and available at https://beagle-dev.github.io.
Identifiants
pubmed: 31034053
pii: 5477405
doi: 10.1093/sysbio/syz020
pmc: PMC6802572
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1052-1061Subventions
Organisme : NIAID NIH HHS
ID : U19 AI135995
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG006139
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI107034
Pays : United States
Organisme : Wellcome Trust
ID : 206298/Z/17/Z
Pays : United Kingdom
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
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