Applications/MrBayes - Revision history

Pysdlb: /* Further Information */

2022-11-16T10:52:43Z

‎Further Information

Pysdlb: /* Navigation */

2022-11-16T10:52:35Z

‎Navigation

Pysdlb at 13:21, 24 May 2019

2019-05-24T13:21:32Z

Chris.collins: /* Executables */

2017-02-08T09:14:56Z

‎Executables

Chris.collins: /* Usage Examples */

2017-02-07T16:41:45Z

‎Usage Examples

Chris.collins: /* Batch Submission */

2017-02-07T16:18:26Z

‎Batch Submission

Chris.collins: /* Application Details */

2017-02-07T16:15:23Z

‎Application Details

Chris.collins: Created page with "TOC === Application Details === * Description: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. Mr..."

2017-02-07T16:14:49Z

Created page with "__TOC__ === Application Details === * Description: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. Mr..."

New page

__TOC__
=== 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: GNU General Public License version 2.0 (GPLv2)

== Usage Examples ==
=== Interactive ===
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[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 >
</pre>
=== 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:

<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J MrBTest
#SBATCH -N 4
#SBATCH -n 100
#SBATCH -o %N-%j.log
#SBATCH -e %N-%j.err
#SBATCH -p compute

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
</pre>

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

<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">
[username@login01 ~]$ sbatch MRBayes.job
Submitted batch job 289555
</pre>

== Further Information ==
* [http://mrbayes.sourceforge.net/ MrBayes website]
* [[Main Page#General_Support|Wiki: General Support]]
* [[Programming/OpenMPI|Wiki: OpenMPI]]
* [[Main Page|Wiki: Home]]

← Older revision		Revision as of 10:52, 16 November 2022
Line 70:		Line 70:


−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 16: / Line 16: @@
 |-
 | mb-mpi
-| OpenMPI parallel version
+| OpenMPI parallel version. Needs to be run with mpirun and following flags '''mpirun -mca pml cm -mca mtl psm2 mb-mpi'''
 |}
 === Interactive ===
 <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

@@ Line 68: / Line 68: @@
 == Further Information ==
 * [http://mrbayes.sourceforge.net/ MrBayes website]
 {{Modulepagenav}}

@@ Line 68: / Line 68: @@
 == Further Information ==
 * [http://mrbayes.sourceforge.net/ MrBayes website]
-* [[Main Page#General_Support|Wiki: General Support]]
-* [[Programming/OpenMPI|Wiki: OpenMPI]]
-* [[Main Page|Wiki: Home]]
+==Navigation==

@@ Line 33: / Line 33: @@
 <pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
 #!/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
@@ Line 46: / Line 46: @@
 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

@@ Line 4: / Line 4: @@
 * Versions: 3.2.6
 * Module names: mrbayes/gcc/3.2.6
-* License: GNU General Public License version 2.0 (GPLv2)
+* License: Available to all; GNU General Public License version 2.0 (GPLv2)
 == Usage Examples ==