Difference between revisions of "Applications/MrBayes"
From HPC
m (→Application Details) |
(→Batch Submission) |
||
Line 33: | Line 33: | ||
<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 | ||
Line 46: | Line 46: | ||
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 | ||
Revision as of 16:18, 7 February 2017
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
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