Difference between revisions of "BEAST"
| Line 48: | Line 48: | ||
* To limit the number of computing cores Beast will use for posterior computation to the number requested from the batch system use the <code>'-threads N'</code> where 'N' is the number of threads. Then, the job resource request should be equal to <code>nodes=1:ppn=X</code> where X = N + 1. | * To limit the number of computing cores Beast will use for posterior computation to the number requested from the batch system use the <code>'-threads N'</code> where 'N' is the number of threads. Then, the job resource request should be equal to <code>nodes=1:ppn=X</code> where X = N + 1. | ||
* General performance considerations - [http://www.beast2.org/beagle-beast-2-in-cluster/ http://www.beast2.org/beagle-beast-2-in-cluster/]. | * General performance considerations - [http://www.beast2.org/beagle-beast-2-in-cluster/ http://www.beast2.org/beagle-beast-2-in-cluster/]. | ||
| + | * Beast2 plugins are installed into your personal directory. This means that you will need to start Beauti and install plugins manually. | ||
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 18:16, 25 January 2021
Description
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
Required Modules
Serial
- beast
System Variables
- HPC_BEAST_DIR - installation directory
- HPC_BEAST_DOC - docs directory
- BEAST - Beast directory
GPU Accelerated BEAST
The latest BEAST-1.x installs have a 'beast-gpu' wrapper that can greatly accelerate some analysis when run in the gpu partition on HiPerGator. 7-20x speedups were observed on a medium-sized test dataset allowing to shorten cycle time for that particular analysis from 1 hour per million states to under 15 minutes and in some cases to under 3 minutes per million states for the majority of the run. Look for the 'beast-gpu' command in a particular beast module like beast/1.10.0.
Galaxy
Beast is also available for use through the friendly web interface of the UFRC Galaxy instance. It's located in the "Phylogenetics" section.
Interactive beauti use
In short, you have to use a SLURM GUI session and specify the module you want as the default beast module could be different from the one you'd like to run.
E.g.
module load gui gui star --module beast/2.6.0 -e beauti
See GUI Programs for reference.
Additional Information
- To use the beagle library use the
'-beagle_SSE -beagle_instances N'command line switches where 'N' equals to the number of requested Beagle library instances. - To limit the number of computing cores Beast will use for posterior computation to the number requested from the batch system use the
'-threads N'where 'N' is the number of threads. Then, the job resource request should be equal tonodes=1:ppn=Xwhere X = N + 1. - General performance considerations - http://www.beast2.org/beagle-beast-2-in-cluster/.
- Beast2 plugins are installed into your personal directory. This means that you will need to start Beauti and install plugins manually.