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BEAGLE

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 3D graphics boards found in many PCs. 

  • The current version of BEAGLE will only work with BEAST v1.6 or later

BEAGLE is an independent project and its website is http://beagle-lib.googlecode.com

Binary installers are now available:

To install on Linux see the following instructions:

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:

When run, it should show a list of available resources that BEAGLE has detected:

BEAGLE resources available:
0 : CPU
Flags: DOUBLE SINGLE ASYNCH SYNCH COMPLEX CPU

1 : GeForce GTX 285
Global memory (MB): 1024
Clock speed (Ghz): 1.48
Number of cores: 240
Flags: SINGLE ASYNCH SYNCH COMPLEX LSCALE GPU

2 : GeForce GT 120
Global memory (MB): 512
Clock speed (Ghz): 1.40
Number of cores: 32
Flags: SINGLE ASYNCH SYNCH COMPLEX LSCALE GPU

This shows the CPU (which should always be available) and two NVidia graphics cards. 

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 BEAGLE will say what resource it is using:

Using BEAGLE TreeLikelihood
Branch rate model used: strictClockBranchRates
resourceNumber = 1
Using BEAGLE resource 1 : GeForce GTX 285
Global memory (MB): 1024
Clock speed (Ghz): 1.48
Number of cores: 240
Flags: SINGLE ASYNCH SYNCH COMPLEX LSCALE GPU

Unless you have a high-specification NVIDIA GPU installed, it is suggested you use the 'Prefer use of: CPU' and 'Prefer precision: double'.

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.