BEAST (and BEAST 2, of course) is widely uesed for phylogenetic inference. But it is quite complicated. This post represents some useful tips while using BEAST.

1. Install beagle-lib

Beagle-lib accelerates Bayesian and Maximun Likelihood phylogenetic software amazingly. Especially the beagle-lib v3.x improves 20-50% than version 2.x.

1.1 Compile beagle-lib without CUDA and OpenCL

Although CUDA and OpenCL improves BEAST computing significantly, how to install beagle-lib without an Nvidia GPU card?

./configure --without-cuda --without-opencl

It will show these warning messages:

configure: WARNING: OpenCL not found or disabled.  OpenCL implementation  will not be built. If OpenCL support is desired, check the path to OpenCL and specify --with-opencl=/path/to/opencl
configure: WARNING: NVIDIA CUDA nvcc compiler not found or CUDA support disabled.  CUDA implementation will not be built. If CUDA support is desired, check the path to CUDA and specify --with-cuda=/path/to/cuda

It’s OK. Simply continue with:

make install

And do not forget run test with:

make check

1.2 Install beagle-lib in custom path

Sometimes it’s not possible to install beagle-lib in the default system library path /usr/local/lib. It could be resolved by setting the environment variable LD_LIBRARY_PATH.

For example, to install beagle-lib into /data/lib, in configure step:

./configure --prefix=/data
make install

Then append to .bashrc:

export LD_LIBRARY_PATH=/data/lib:$LD_LIBRARY_PATH

Then run

source .bashrc

to enable the environment change.