Using BEAGLE with BEAST
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. It can make use of highly-parallel processors such as those in graphics processing units (GPUs) found in many PCs.
The current version of BEAGLE will only work with BEAST v1.6 or later
Download Mac OS X Tiger 10.4 ISO Windows had been struggling to enable the same graphic settings into their systems but apple did it effortlessly. The Mac OS X Tiger was one of the record-breaking operating systems that made the cut of making the line up of Mac OS X popular among Mac users. Click here to download a simple shell script for dividing your sample. Two specialized programs, pseudomarker.jar and cluster2haps.jar are described in the BEAGLE documentation, and may be useful to some users: pseudomarker.jar - A utility program for creating a phased Beagle file of pseudomarkers from a Beagle output model (.dag) file.
Downloading and installing BEAGLE
BEAGLE is an independent project and its website is https://github.com/beagle-dev/beagle-lib, where binary installers and installation instructions for different operating systems are available.
Testing the BEAGLE installation
To test the installation, run BEAST and when the options dialog box appears, select “Use BEAGLE library” and “Show list of available BEAGLE resources”:
You don’t need to specify a BEAST input file as the information about BEAGLE will be displayed and then BEAST will stop. For the commandline version of BEAST, type:
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When run, it should show a list of available resources that BEAGLE has detected:
This shows the CPU (which should always be available), an Intel integrated graphics processor (this is the graphics chip that is used to run the computer display) and one NVidia Tesla GPU card specifically designed for scientific computing.
Running BEAST with BEAGLE
You are now ready to run BEAST using BEAGLE. Just run BEAST again and select “Use BEAGLE library” but not the “Show list of available BEAGLE resources” option. When running, as part of the initial pre-amble text, BEAGLE will say what resource it is using:
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This shows that BEAGLE will be using the primary CPU and gives some details about the options it will be using. The default options will be optimal for most machines but see this page for information about optimizing BEAST computational performance.
Running BEAST/BEAGLE on command line
If you are running BEAST on Linux or wish to have more control of the BEAGLE performance options on Mac OS X or Windows you will need to run BEAST from the command line.
Running BEAST from the command line allows you to select which resource needs to be used for your analysis by using a command-line option.For example, in order to ensure that resource 1 (see above) will be used when running BEAST, you can use the following command:
The full list of command-line BEAGLE options can be listed using
beast -help and are listed here:
Frequently Asked Questions
When attempting to run BEAST with BEAGLE, I get the following error message and BEAST/BEAGLE crashes:
This isn’t so much a BEAGLE error as it is a compatibility problem with the operating system and the Java installation. Notice how the error message mentions a mixed mode installation, which usually indicates that a 32-bit Java version was installed on a 64-bit Windows operating system. Upgrading the 32-bit Java installation to a 64-bit version usually fixes this problem.
Upon building the BEAGLE library from source, I get the following error message when running the
This can be fixed by correctly setting the
JAVA_HOMEvariable. For example, on a MacBook running Java version 8 Update 121, this can be done as follows:
When running BEAST using the installation packages (i.e. BEAST v1.10.0.app on Mac OS and BEAST v1.10.0.exe on Windows), the BEAGLE installation cannot be found:
Possibly, the issue here is that you’re using the installation packages for BEAST but have installed BEAGLE from its source files (i.e. Download cpu z for mac windows 10. not using BEAGLE’s installation package). At the moment, it’s indeed not readily possible to combine these two approaches and we suggest to either use the installation packages for both BEAST and BEAGLE or to build both from source.
A manuscript describes the BEAGLE API and library: http://sysbio.oxfordjournals.org/content/61/1/170
The paper describing the algorithms used for calculating likelihoods of sequences on trees using many core devices like graphics processing units (GPUs) is available from: https://academic.oup.com/bioinformatics/article/25/11/1370/332982
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