BEAST

BEAST is a program for the analysis of molecular sequences using Baysian Markov chain Monte Carlo methods. It can be used together with the BEAGLE library, which provides optimised routines for Baysian and Maximum Likelihood calculations and can make use of GPUs.

If a GPU is required, this must be requested as a generic resource via the option --gres, as shown in the example below:

#SBATCH --job-name=beast_beagle
#SBATCH --mail-user=your.name@fu-berlin.de
#SBATCH --mail-type=end

#SBATCH --partition=gpu
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --mem=5000
#SBATCH --time=1-00:00:00

module load beagle beast

cd /scratch/yourname/beast/

beast_beagle -overwrite -beagle_GPU data.xml > output.txt

Here the generic resource is gpu and the number of resources is 1. Note that it is also necessary to specify the BEAST option -beast_GPU.