Please see: http://www.beast2.org/performance-suggestions/index.html for information about optimizing performance. The BEAGLE libraries will be available when you load the BEAST module and BEAGLE is enabled used by default. There are BEAGLE options such as -beage_SSE which may help performance.
To add a beast add-on use the following command after you've loaded the beast module (
module load bioinformatics/beast) first list available add-ons:
and then add one with
packagemanager -add SNAPP
The add-on will be downloaded to ~/.beast