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:
And do not forget run test with:
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
For example, to install beagle-lib into /data/lib, in configure step:
./configure --prefix=/data make install
Then append to .bashrc:
to enable the environment change.