{"id":3104,"date":"2016-06-14T09:06:51","date_gmt":"2016-06-14T09:06:51","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=3104"},"modified":"2016-07-22T12:36:14","modified_gmt":"2016-07-22T12:36:14","slug":"mrbayes","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/mrbayes\/","title":{"rendered":"MrBayes"},"content":{"rendered":"

Overview<\/h2>\n

MrBayes<\/a> is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.<\/p>\n

Version 3.2.6 and 3.2.5 are installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on access on the CSF – the software is made available under the GNU GPL v3 license<\/a>. If you use this software in your research please cite it. Run the command citations<\/code> in the software for further details.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

\r\n# Parallel (MPI) versions for multi-node (large MPI jobs - using fast InfiniBand network)\r\napps\/gcc\/mrbayes\/3.2.6-mpi-ib\r\napps\/gcc\/mrbayes\/3.2.6-beagle-mpi-ib\r\n\r\n# Parallel (MPI) versions for single-node (small MPI jobs)\r\napps\/gcc\/mrbayes\/3.2.6-mpi\r\napps\/gcc\/mrbayes\/3.2.6-beagle\r\n\r\n# Serial (1 core) version\r\napps\/gcc\/mrbayes\/3.2.6\r\n\r\n# Parallel (MPI) only\r\nmodule load apps\/gcc\/mrbayes\/3.2.5\r\n<\/pre>\n
The beagle<\/code> versions of the modulefiles load a version of MrBayes that has been compiled against the Beagle<\/a> library. You run this version in the same way as all other versions but may see some speed-up depending on the features you used in MrBayes. Please consult the MrBayes<\/a> manual for more information. <\/p>\n
Running the application<\/h2>\n
Please do not run MrBayes on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\nmb myinput.nex\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Small Single-node Parallel batch job submission<\/h3>\n
This assume you have loaded one of the -mpi<\/code> modulefiles. The number of cores should be no more than 24. Note that the parallel version of the MrBayes executable is named<\/p>\n
\r\npmb\r\n<\/pre>\n
An example jobscript is:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 16    # Single node parallel (up to 24 cores can be used)\r\n\r\n# $NSLOTS is automatically set to the number of cores requested above\r\nmpirun -n $NSLOTS pmb myinput.nex\r\n                   #\r\n                   #\r\n                   # Note that the executable is now 'pmb' not 'mb'\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Large Multi-node Parallel batch job submission<\/h3>\n
This assume you have loaded one of the -mpi-ib<\/code> modulefiles. The number of cores must be a multiple of 24. Note that the parallel version of the MrBayes executable is named<\/p>\n
\r\npmb\r\n<\/pre>\n
An example jobscript is:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd               # Job will run from the current directory\r\n#$ -V                 # Job will inherit current environment settings\r\n#$ -pe orte-24-ib 48  # Multi node parallel job (number of cores must be a multiple of 24).\r\n\r\n# $NSLOTS is automatically set to the number of cores requested above\r\nmpirun -n $NSLOTS pmb myinput.nex\r\n                   #\r\n                   #\r\n                   # Note that the executable is now 'pmb' not 'mb'\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Interactive use for Development<\/h3>\n
MrBayes provides an interactive command-line which can be used for testing and developing your scripts. Please do not<\/strong> run MrBayes on the login node. Instead you should request an interactive session on a compute node as follows:<\/p>\n
\r\nqrsh -l inter -l short\r\n  # Wait for an interactive session to start. If no resources\r\n  # are free you will be asked to try again later.\r\n\r\n# Now on the backend compute-node load the modulefile\r\nmodule load apps\/gcc\/mrbayes\/version<\/em>\r\n\r\n# Start the interactive shell\r\nmb\r\n\r\n# When you have finished with your interactive session, return to login node;\r\nexit\r\n<\/pre>\n
Example Scripts<\/h3>\n
After loading one of the modulefiles, example scripts are available in the directory:<\/p>\n
\r\n$MRBAYES_HOME\/examples\/\r\n<\/pre>\n
Further info<\/h2>\n