Revbayes is an application for Bayesian phylogenetic inference, and includes an MPI implementation. According to the authors:

RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. However, the environment is quite general and can be useful for many complex modeling tasks.

RevBayes uses its own language, Rev, which is a probabilistic programming language like JAGS, STAN, Edward, PyMC3, and related software. However, phylogenetic models require inference machinery and distributions that are unavailable in these other tools.

The Rev language is similar to the language used in R. Like the R language, Rev is designed to support interactive analysis. It supports both functional and procedural programming models, and makes a clear distinction between the two. Rev is also more strongly typed than R.

References:

• Höhna, Landis, Heath, Boussau, Lartillot, Moore, Huelsenbeck, Ronquist. 2016 RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language Systematic Biology, 65:726-736.
• Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63:753–771.

• Revbayes main site
• RevBayes Tutorials.

• Module Name: revbayes (see the modules page for more information)
• Singlethreaded and MPI
• Environment variables set
  • RB_EXAMPLE_DATA set to /usr/local/apps/revabyes/example-data which includes tutorial data available here

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load revabyes

[user@cn3144 ~]$ cp -r $RB_EXAMPLE_DATA/RB_Partition_Tutorial .

[user@cn3144 ~]$ cd RB_Partition_Tutorial

[user@cn3144 ~]$ rb scripts/mcmc_Partition_uniform.Rev

RevBayes version (1.1.1)
Build from development (rapture-641-g7d4aab) on Tue Mar  9 13:42:53 EST 2021

Visit the website www.RevBayes.com for more information about RevBayes.

RevBayes is free software released under the GPL license, version 3. Type 'license()' for details.

To quit RevBayes type 'quit()' or 'q()'.


> source("scripts/mcmc_Partition_uniform.Rev")
   Processing file "scripts/mcmc_Partition_uniform.Rev"
   Successfully read one character matrix from file 'data/primates_and_galeopterus_cox2.nex'
   Successfully read one character matrix from file 'data/primates_and_galeopterus_cytb.nex'

   Running burn-in phase of Monte Carlo sampler for 10000 iterations.
   This simulation runs 2 independent replicates.
   The simulator uses 52 different moves in a random move schedule with 62 moves per iteration

Progress:
0---------------25---------------50---------------75--------------100
********************************************************************


   Running MCMC simulation
   This simulation runs 2 independent replicates.
   The simulator uses 52 different moves in a random move schedule with 62 moves per iteration

Iter        |      Posterior   |     Likelihood   | ...
----------------------------------------------------...
0           |       -21259.5   |       -21227.8   | ...
1000        |       -21273.7   |       -21241.1   | ...
[...]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. revbayes.sh). For example:

#!/bin/bash
set -e
module load revbayes
cd /data/$USER/analysis_dir/
rb scripts/full_analysis.Rev

Submit this job using the Slurm sbatch command. Since this is the singlethreaded version, you do not need to update the number of CPUs allocated.

sbatch [--mem=#] revbayes.sh

Create a swarmfile (e.g. revbayes.swarm). For example:

rb script/mcmc_model1.Rev
rb script/mcmc_model2.Rev
rb script/mcmc_model3.Rev
[...]

Submit this job using the swarm command.

swarm -f revbayes.swarm [-g #] --module revbayes

An MPI job can run in parallel across multiple nodes. We highly recommend reading our guidelines on multinode jobs. Set up a batch script, e.g. revbayes-mpi.sh, along the following lines:

  #!/bin/bash
  #SBATCH --partition=multinode
  #SBATCH --constraint=x2695
  #SBATCH --ntasks=8
  #SBATCH --ntasks-per-core=1
  #SBATCH --mem-per-cpu=1G
  #SBATCH --time=2:00:00
  
  module load revbayes
  
  WDIR=/data/$USER/analysis_dir
  
  cd $WDIR
  
  mpirun -np $SLURM_NTASKS rb-mpi scripts/full_analysis.Rev

sbatch revbayes-mpi.sh