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BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical
Daniel L Ayres1, Michael P Cummings1, Guy Baele2
1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
Systematic Biology
|April 30, 2019
Summary
BEAGLE 3 enhances phylogenetic inference speed with new parallel computing methods. This open-source library offers significant performance gains for evolutionary analyses on diverse hardware.
Area of Science:
- Computational Biology
- Evolutionary Biology
- Bioinformatics
Background:
- BEAGLE is a high-performance library for phylogenetic inference.
- It features a flexible API and efficient implementations for various evolutionary models and hardware.
- BEAGLE is integrated into popular software like BEAST and MrBayes, widely used in evolutionary studies.
Purpose of the Study:
- Introduce BEAGLE 3, highlighting its new parallel implementations and performance enhancements.
- Improve scalability, usability, and hardware utilization for phylogenetic analyses.
- Provide developers with resources for integrating the library.
Main Methods:
- Implemented new OpenCL and CPU-threaded versions for broader hardware support.
- Extended the API to enable concurrent computation of partial likelihood arrays.
- Optimized integration with phylogenetic software for multi-GPU and cluster environments.
- Developed an automated device selection method based on data, model, and hardware.
Main Results:
- Achieved up to 5.9-fold runtime performance improvement in partitioned analyses compared to previous GPU versions.
- Demonstrated increased performance for challenging datasets and improved scalability.
- Enabled more flexible data partitioning and concurrent computation for nucleotide models.
Conclusions:
- BEAGLE 3 offers substantial performance and usability improvements for phylogenetic inference.
- The library effectively leverages modern hardware, including GPUs and clusters.
- BEAGLE 3 is a valuable, free, and open-source tool for the evolutionary biology community.
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