schliessen

Filtern

 

Bibliotheken

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

Abstract 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 o... Full description

Journal Title: Systematic biology 2019, Vol.68 (6), p.1052-1061
Main Author: Ayres, Daniel L
Other Authors: Cummings, Michael P , Baele, Guy , Darling, Aaron E , Lewis, Paul O , Swofford, David L , Huelsenbeck, John P , Lemey, Philippe , Rambaut, Andrew , Suchard, Marc A
Format: Electronic Article Electronic Article
Language: English
Subjects:
GPU
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/31034053
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6802572
title: BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics
format: Article
creator:
  • Ayres, Daniel L
  • Cummings, Michael P
  • Baele, Guy
  • Darling, Aaron E
  • Lewis, Paul O
  • Swofford, David L
  • Huelsenbeck, John P
  • Lemey, Philippe
  • Rambaut, Andrew
  • Suchard, Marc A
subjects:
  • Bayesian phylogenetics
  • Classification - methods
  • Data Interpretation, Statistical
  • Evolution
  • GPU
  • maximum likelihood
  • multicore processing
  • parallel computing
  • Phylogeny
  • Software - standards
  • Software for Systematics
  • Software for Systematics and Evolution
ispartof: Systematic biology, 2019, Vol.68 (6), p.1052-1061
description: Abstract 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.
language: eng
source:
identifier: ISSN: 1063-5157
fulltext: no_fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


@attributes
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
RANK2.755112
LOCALfalse
PrimoNMBib
record
control
sourceidproquest_pubme
recordidTN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6802572
sourceformatXML
sourcesystemPC
oup_id10.1093/sysbio/syz020
sourcerecordid2216773455
originalsourceidFETCH-LOGICAL-1590t-f8d1af5bf66c8059a003d6f057fc630ab2b8d4a03ed9e7801c64873f80dcb2660
addsrcrecordideNqFkk1rFDEYgAdRbK0evUqOHjr6ZjLJJB6EuqztwqKFWvAW8rkbmZlsJ7OVFfzvZpm1tIJ6SkKePHm_iuIlhjcYBHmbdkmHmJcfUMGj4hhDw0pO2NfH-z0jJcW0OSqepfQNAGNG8dPiiGAgNVByXPz8MD87X84ReYcW3WaIt86iSzf4OHSqN-4UXRnVhn51ilRv0XVSOrRh3KEMIIUuwmpd3sPRLHab7Zh5tAx6UMMEXo1qDGkMWYUu17s2rlzv8jE9L5541Sb34rCeFNcf519mF-Xy8_lidrYsMRUwlp5brDzVnjHDgQoFQCzzQBtvGAGlK81trYA4K1zDARtW84Z4DtboijE4Kd5P3s1Wd84a14-DauVmCF2OUUYV5MObPqzlKt5KxqGiTZUFi0kQN65XYXAP3tqcjYxWEhC1bKwFSw3zwhmDtWCCca2tBop53dgmuz79z2Wd3W7kdy9zy2SlrOaVEII32grNgHgiTF0JTjzWNWTh60N2Q7zZujTKLiTj2lb1Lm6TrCrMmobUlGa0nFAzxJQG5-_-xiD38ySneZLTPGX-1f3C3dG_BygD5A-hCftux30dQ_tX7SHimNP8dwS_AAMy6U0
sourcetypeOpen Access Repository
isCDItrue
recordtypearticle
pqid2216773455
display
typearticle
titleBEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics
creatorAyres, Daniel L ; Cummings, Michael P ; Baele, Guy ; Darling, Aaron E ; Lewis, Paul O ; Swofford, David L ; Huelsenbeck, John P ; Lemey, Philippe ; Rambaut, Andrew ; Suchard, Marc A
contributorPosada, David
creatorcontribAyres, Daniel L ; Cummings, Michael P ; Baele, Guy ; Darling, Aaron E ; Lewis, Paul O ; Swofford, David L ; Huelsenbeck, John P ; Lemey, Philippe ; Rambaut, Andrew ; Suchard, Marc A ; Posada, David
descriptionAbstract 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.
identifier
0ISSN: 1063-5157
1EISSN: 1076-836X
2DOI: 10.1093/sysbio/syz020
3PMID: 31034053
languageeng
publisherEngland: Oxford University Press
subjectBayesian phylogenetics ; Classification - methods ; Data Interpretation, Statistical ; Evolution ; GPU ; maximum likelihood ; multicore processing ; parallel computing ; Phylogeny ; Software - standards ; Software for Systematics ; Software for Systematics and Evolution
ispartofSystematic biology, 2019, Vol.68 (6), p.1052-1061
rights
0The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. 2019
1The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
lds50peer_reviewed
oafree_for_read
citedbyFETCH-LOGICAL-1590t-f8d1af5bf66c8059a003d6f057fc630ab2b8d4a03ed9e7801c64873f80dcb2660
citesFETCH-LOGICAL-1590t-f8d1af5bf66c8059a003d6f057fc630ab2b8d4a03ed9e7801c64873f80dcb2660
links
openurl$$Topenurl_article
thumbnail$$Usyndetics_thumb_exl
backlink$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31034053$$D View this record in MEDLINE/PubMed
search
contributorPosada, David
creatorcontrib
0Ayres, Daniel L
1Cummings, Michael P
2Baele, Guy
3Darling, Aaron E
4Lewis, Paul O
5Swofford, David L
6Huelsenbeck, John P
7Lemey, Philippe
8Rambaut, Andrew
9Suchard, Marc A
title
0BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics
1Systematic biology
addtitleSyst Biol
descriptionAbstract 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.
subject
0Bayesian phylogenetics
1Classification - methods
2Data Interpretation, Statistical
3Evolution
4GPU
5maximum likelihood
6multicore processing
7parallel computing
8Phylogeny
9Software - standards
10Software for Systematics
11Software for Systematics and Evolution
issn
01063-5157
11076-836X
fulltextfalse
rsrctypearticle
creationdate2019
recordtypearticle
recordideNqFkk1rFDEYgAdRbK0evUqOHjr6ZjLJJB6EuqztwqKFWvAW8rkbmZlsJ7OVFfzvZpm1tIJ6SkKePHm_iuIlhjcYBHmbdkmHmJcfUMGj4hhDw0pO2NfH-z0jJcW0OSqepfQNAGNG8dPiiGAgNVByXPz8MD87X84ReYcW3WaIt86iSzf4OHSqN-4UXRnVhn51ilRv0XVSOrRh3KEMIIUuwmpd3sPRLHab7Zh5tAx6UMMEXo1qDGkMWYUu17s2rlzv8jE9L5541Sb34rCeFNcf519mF-Xy8_lidrYsMRUwlp5brDzVnjHDgQoFQCzzQBtvGAGlK81trYA4K1zDARtW84Z4DtboijE4Kd5P3s1Wd84a14-DauVmCF2OUUYV5MObPqzlKt5KxqGiTZUFi0kQN65XYXAP3tqcjYxWEhC1bKwFSw3zwhmDtWCCca2tBop53dgmuz79z2Wd3W7kdy9zy2SlrOaVEII32grNgHgiTF0JTjzWNWTh60N2Q7zZujTKLiTj2lb1Lm6TrCrMmobUlGa0nFAzxJQG5-_-xiD38ySneZLTPGX-1f3C3dG_BygD5A-hCftux30dQ_tX7SHimNP8dwS_AAMy6U0
startdate20191101
enddate20191101
creator
0Ayres, Daniel L
1Cummings, Michael P
2Baele, Guy
3Darling, Aaron E
4Lewis, Paul O
5Swofford, David L
6Huelsenbeck, John P
7Lemey, Philippe
8Rambaut, Andrew
9Suchard, Marc A
general
0Oxford University Press
1OXFORD UNIV PRESS
scope
0TOX
1CGR
2CUY
3CVF
4ECM
5EIF
6NPM
7AAYXX
8CITATION
97X8
10BOBZL
11CLFQK
125PM
sort
creationdate20191101
titleBEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics
authorAyres, Daniel L ; Cummings, Michael P ; Baele, Guy ; Darling, Aaron E ; Lewis, Paul O ; Swofford, David L ; Huelsenbeck, John P ; Lemey, Philippe ; Rambaut, Andrew ; Suchard, Marc A
facets
frbrtype5
frbrgroupidcdi_FETCH-LOGICAL-1590t-f8d1af5bf66c8059a003d6f057fc630ab2b8d4a03ed9e7801c64873f80dcb2660
rsrctypearticles
prefilterarticles
languageeng
creationdate2019
topic
0Bayesian phylogenetics
1Classification - methods
2Data Interpretation, Statistical
3Evolution
4GPU
5maximum likelihood
6multicore processing
7parallel computing
8Phylogeny
9Software - standards
10Software for Systematics
11Software for Systematics and Evolution
toplevelpeer_reviewed
creatorcontrib
0Ayres, Daniel L
1Cummings, Michael P
2Baele, Guy
3Darling, Aaron E
4Lewis, Paul O
5Swofford, David L
6Huelsenbeck, John P
7Lemey, Philippe
8Rambaut, Andrew
9Suchard, Marc A
collection
0Oxford Journals Open Access Collection
1Medline
2MEDLINE
3MEDLINE (Ovid)
4MEDLINE
5MEDLINE
6PubMed
7CrossRef
8MEDLINE - Academic
9OpenAIRE (Open Access)
10OpenAIRE
11PubMed Central (Full Participant titles)
jtitleSystematic biology
delivery
delcategoryRemote Search Resource
fulltextno_fulltext
addata
au
0Ayres, Daniel L
1Cummings, Michael P
2Baele, Guy
3Darling, Aaron E
4Lewis, Paul O
5Swofford, David L
6Huelsenbeck, John P
7Lemey, Philippe
8Rambaut, Andrew
9Suchard, Marc A
formatjournal
genrearticle
ristypeJOUR
atitleBEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics
jtitleSystematic biology
addtitleSyst Biol
date2019-11-01
risdate2019
volume68
issue6
spage1052
epage1061
pages1052-1061
issn1063-5157
eissn1076-836X
abstractAbstract 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.
copEngland
pubOxford University Press
pmid31034053
doi10.1093/sysbio/syz020
oafree_for_read