Difference between revisions of "Applications/MrBayes"
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== Usage Examples == | == Usage Examples == | ||
| + | === Executables === | ||
| + | {| class="wikitable" style="background-color:#f5f5dc;" | ||
| + | ! Executable | ||
| + | ! Description | ||
| + | |- | ||
| + | | mb | ||
| + | | Single core and/or interactive | ||
| + | |- | ||
| + | | mb-mpi | ||
| + | | OpenMPI parallel version. Needs to be run with mpirun and following flags '''mpirun -mca pml cm -mca mtl psm2 mb-mpi''' | ||
| + | |} | ||
| + | |||
=== Interactive === | === Interactive === | ||
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
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<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;"> | <pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;"> | ||
#!/bin/bash | #!/bin/bash | ||
| − | #SBATCH -J MrBTest | + | #SBATCH -J MrBTest # Job name, you can change it to whatever you want |
| − | #SBATCH -N 4 | + | #SBATCH -N 4 # Number of nodes to run across |
| − | #SBATCH -n 100 | + | #SBATCH -n 100 # Number of cores to run across |
| − | #SBATCH -o %N-%j.log | + | #SBATCH -o %N-%j.log # Standard output will be written here |
| − | #SBATCH -e %N-%j.err | + | #SBATCH -e %N-%j.err # Standard error will be written here |
| − | #SBATCH -p compute | + | #SBATCH -p compute # Slurm partition, where you want the job to be queued |
module add openmpi/gcc/1.10.5 mrbayes/gcc/3.2.6 | module add openmpi/gcc/1.10.5 mrbayes/gcc/3.2.6 | ||
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The options for mpirun are required to make use of the Omni-Path interconnect. | The options for mpirun are required to make use of the Omni-Path interconnect. | ||
| + | |||
This submission script can be found at /path/to/sample/script | This submission script can be found at /path/to/sample/script | ||
| Line 55: | Line 68: | ||
== Further Information == | == Further Information == | ||
* [http://mrbayes.sourceforge.net/ MrBayes website] | * [http://mrbayes.sourceforge.net/ MrBayes website] | ||
| − | + | ||
| − | + | {{Modulepagenav}} | |
| − | |||
Latest revision as of 10:52, 16 November 2022
Contents
Application Details
- Description: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
- Versions: 3.2.6
- Module names: mrbayes/gcc/3.2.6
- License: Available to all; GNU General Public License version 2.0 (GPLv2)
Usage Examples
Executables
| Executable | Description |
|---|---|
| mb | Single core and/or interactive |
| mb-mpi | OpenMPI parallel version. Needs to be run with mpirun and following flags mpirun -mca pml cm -mca mtl psm2 mb-mpi |
Interactive
[username@c170 ~]$ mb
MrBayes v3.2.6 x64
(Bayesian Analysis of Phylogeny)
Distributed under the GNU General Public License
Type "help" or "help <command>" for information
on the commands that are available.
Type "about" for authorship and general
information about the program.
MrBayes >
Batch Submission
A better approach is to submit a MrBayes task as a parallel batch submission to run across multiple nodes, an example of which is:
#!/bin/bash #SBATCH -J MrBTest # Job name, you can change it to whatever you want #SBATCH -N 4 # Number of nodes to run across #SBATCH -n 100 # Number of cores to run across #SBATCH -o %N-%j.log # Standard output will be written here #SBATCH -e %N-%j.err # Standard error will be written here #SBATCH -p compute # Slurm partition, where you want the job to be queued module add openmpi/gcc/1.10.5 mrbayes/gcc/3.2.6 mpirun -mca pml cm -mca mtl psm2 mb-mpi input_nex_file.nex
The options for mpirun are required to make use of the Omni-Path interconnect.
This submission script can be found at /path/to/sample/script
[username@login01 ~]$ sbatch MRBayes.job Submitted batch job 289555