RevBayes
RevBayes is a program for Bayesian phylogenetic inference. Models are specified as probabilistic graphical models in Rev, an interpreted language similar to R, which makes it possible to build and combine a wide range of phylogenetic and evolutionary models.
License
Free to use and open source under GNU GPLv3.
Available
- Roihu-CPU: 1.4.1, via the
bio-appsmodule.
Usage
RevBayes is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the RevBayes module:
On Roihu, RevBayes is built with MPI support and the command is rb-mpi; there is
no separate rb command. Run a Rev script with:
Started without a script, rb-mpi opens the interactive Rev console. Run the console
and short tests in an interactive session,
not on the login node.
Running in parallel
When launched with srun in a batch job, RevBayes divides the independent replicates
of an analysis (the nruns argument of mcmc() and mcmcmc()) and the stones of a
power-posterior analysis among the MPI processes. Use as many processes as there are
replicates, for example 4 processes for nruns=4.
Example batch script
#!/bin/bash
#SBATCH --job-name=revbayes
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2G
module load bio-apps/v202603
module load revbayes/1.4.1
srun rb-mpi my_analysis.Rev
This example runs four MPI processes, one for each replicate of an analysis with
nruns=4. Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.