BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics
Year: 2019
Type: article
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.
Source: Systematic Biology
Institutions: University of Maryland, College Park, Rega Institute for Medical Research, KU Leuven, University of Technology Sydney, University of Connecticut, Florida Museum of Natural History, University of Florida, University of California, Berkeley, National Institutes of Health, Fogarty International Center, University of Edinburgh, University of California, Los Angeles
Language: English
Subfield: Hardware and Architecture
Field: Computer Science
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $2,364
Awards: G1193641635, G1407748555, Estimating the Bayesian Phylogenetic Information Content of Systematic Data, ABI: Development: Parallel Computing for Phylogenetics: Grid, Public and GPU Computing, G2674448505, G339059223, G3974610566, Putting genomic surveillance at the heart of viral epidemic response., ABI Development: Increasing concurrency for improved performance of the BEAGLE library, Advancing the Molecular Epidemiology of Infectious Diseases through Bayesian Phylogenetics, G6232798251, Putting genomic surveillance at the heart of viral epidemic response., Genomics, EHRs, GPUs, and Next Generation Computational Statistics, Bayesian Modeling and Data Integration in Infectious Disease Phylodynamics, Center for Viral Systems Biology (CViSB)
OpenAlex ID: W2941807936