Connecting Infrastructure, Connecting Research

MrBayes

Description
This description comes from the MrBayes home page. "MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees....more"
Site	Version (Latest: v3.1.2)	Notes
ngs.rl.ac.uk	v3.1.2	Compiled using gcc 3.4.6 and ScaliMPI

License

The following license conditions were copied from the MrBayes documentation wiki in July 2008. You should refer to this page for up to date information.

"MrBayes is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. The program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License (http://www.gnu.org/copyleft/gpl.html) for more details."

When publishing your work using MrBayes on the NGS, you should both credit the NGS and refer to the citation suggestions on the MrBayes wiki site. You should also credit the NGS site where you ran the code.

Running MrBayes on the NGS

Please note that MrBayes has no check point/restart capabilities. This means that the longest run of MrBayes on the NGS will be 48 hours elapsed (Either 1 CPU for 48 hours or 32 CPUs for 48 hours). Runs longer that this may be truncated by sites running the code and no results returned. The max wall clock policies are set by the member sites of the NGS and are set to ensure fair usage of the service for all users

The example input files for all the following submission examples, batch.nex which calls primates.nex, can be found at gsiftp://ngs.rl.ac.uk:2811/apps/MrBayes/examples/batch.nex and primates.nex,

Submission Using the UI/WMS

To submit MrBayes job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

glite-wms-job-submit -o jobIDs -a mrbayes.jdl

Type = "Job";
JobType = "normal";
# To run in MPI mode comment out above line and uncomment following 2
#JobType = "mpich";
#CpuNumber = 2;
Executable = "/usr/ngs/MRBAYES";
Arguments = "batch.nex";
StdOutput = "primates.out";
StdError = "primates.err";
Myproxyserver= "myproxy.ngs.ac.uk";
InputSandbox = {"batch.nex","primates.nex"};
InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/mrbayes";
OutputSandbox = {"primates.err","primates.out"};
OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/mrbayes";
Requirements = (
     member("NGS-UEE-MRBAYES", other.GlueHostApplicationSoftwareRunTimeEnvironment)
);
ShallowRetryCount = -1;

NGS Web Portal Submission
After logging in to the NGS portal, select the "MrBayes" template under the " Bioinformatics" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.
Submission Using Globus
Both the serial and parallel mpi versions of MrBayes are launched in the same way on the NGS. Specifying (jobType=mpi) and (count=2) or more, will launch the mpi version. Using (jobType=single) launches the serial version.

To submit a MrBayes serial job for example on ngs.rl.ac.uk use the following command (one line NOT including the
backslashes '\'):

globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
'&(executable=/usr/ngs/MRBAYES) \
(arguments= batch.nex)(jobType=single) \
(directory=/home/ngsXXXX/mrbayes) \
(stdout=primates.stdout)(stderr=primates.stderr)'
- This runs the default version. To run 1.2 use MRBAYES_3_1_2 instead of MRBAYES.
- stdout and stderr are set to 'primates.stdout' and 'primates.stderr' respectively.
- The first argument must be the program we want to run. (batch.nex in this case)
- The input files must be given as an argument and not as stdin.
- Replace 'ngsXXXX' by your user id on the system running the job (ngs.rl.ac.uk in this case). 'directory' is the working directory for the job, in this case a subdirectory of your homedir called 'mrbayes'
To submit a MrBayes MPI parallel job use the following command (one line NOT including the backslashes '\'):

globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
'&(executable=/usr/ngs/MRBAYES) \
(arguments= batch.nex)(jobType=mpi)(count=4) \
(directory=/home/ngsXXXX/mrbayes) \
(stdout=primates.stdout)(stderr=primates.stderr)'

where all parameters are the same as serial run except :
- 'count' should be always set to the number of processors required (4 in this case).
- 'jobType=mpi' triggers the parallel version of the code.

Compilation Information

Both serial and MPI versions of MrBayes were compiled using gcc 3.4.6. The MPI library used on ngs.rl.ac.uk is ScaliMPI using Myrinet gm libraries.

Further Information

Applications Support

The NGS cannot offer scientific support for applications. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.

Acknowledgements

Please note: When publishing work based on use of the NGS, users should acknowledge both the authors of any programs used (see the individual program web sites, or contact the authors directly) and the NGS directly using the following line:
"The authors would like to acknowledge the use of the UK National Grid Service in carrying out this work"
This line must also accompany any use of the NGS logos.

Primary links