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LinuxInstallInstructions
To install BEAGLE on Linux-based operating systems you will need to build BEAGLE from source.
You can either do this in the manual approach -as described below- or use an automated tool such as EasyBuild, especially useful if you are into the business of using alternative compilers and toolchains, including GPUs etc: Example build options: https://github.com/hpcugent/easybuild-easyconfigs/tree/master/easybuild/easyconfigs/b/beagle-lib
You will need the following software to download and build BEAGLE from source:
- gcc (or other equivalent compiler)
- cmake
- autoconf
- automake
- libtool
- subversion
- pkg-config
Additionally we recommended installing the following optional prerequisites:
- OpenCL implementations for your hardware resources
- NVIDIA CUDA drivers and toolkit (if you want to use BEAGLE with CUDA on an NVIDIA GPU)
- Java JDK (if you want to use BEAGLE with BEAST)
The prerequisite software should be fairly easy to install. On Ubuntu and other Debian Linux distributions all the requisite software can be obtained via apt-get:
sudo apt-get install cmake build-essential autoconf automake libtool git pkg-config openjdk-9-jdk
OpenCL implementations are available from:
- Intel http://software.intel.com/en-us/vcsource/tools/opencl-sdk
- AMD https://github.com/RadeonOpenCompute/ROCm
- NVIDIA https://developer.nvidia.com/opencl
The NVIDIA CUDA drivers and toolkit can be downloaded from http://www.nvidia.com/object/cuda_get.html. They need to be installed for BEAGLE to use CUDA for GPU acceleration.
git clone --depth=1 https://github.com/beagle-dev/beagle-lib.git
cd beagle-lib
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=$HOME ..
make install
This will compile and install the library into $HOME/lib, you can find them by ls -lt $HOME/lib/*beagle*.
If you followed the instructions above, then BEAGLE was installed to your home directory. You'll need to tell other programs to find the beagle library in your home directory by setting the LD_LIBRARY_PATH environment variable:
export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH
Or if using tcsh:
setenv LD_LIBRARY_PATH $HOME/lib:$LD_LIBRARY_PATH
That command will need to be run every time you log in, so it's best to put it in a login script such as .bashrc or .profile or .cshrc, etc.
If you plan to build other applications that depend on beagle, you'll also need be sure BEAGLE is in your pkg-config path:
export PKG_CONFIG_PATH=$HOME/lib/pkgconfig:$PKG_CONFIG_PATH
This too can be put in a login script.
You are now ready to use BEAGLE with compatible applications such as BEAST, MrBayes, and GARLI.
For instructions on how to use BEAGLE with BEAST please refer to Using BEAGLE with BEAST