From BEAST Software
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.