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Using Mr. Bayes on the CCLS HPC Dell Cluster

Versions of Mr. Bayes Installed on the CCLS Cluster

There are two versions of Mr. Bayes installed on the CCLS HPC Dell Cluster:

  1. One optimized for cluster use: cluster-mb
  2. One optimized for single-processor use: mb

mb is the easier of the two to use, as it does not require the initialization or shut-down of the LAM run-time environment.

Using mb

Interactively

sh UNIX Shell Command Example interactive usage of mb 
[mikewong @ccls ~]$ mb


                               MrBayes v3.1.2

                      (Bayesian Analysis of Phylogeny)

                                     by

                  Fredrik Ronquist and John P. Huelsenbeck

                       School of Computational Science
                           Florida State University
                            ronquist@csit.fsu.edu

                 Section of Ecology, Behavior and Evolution
                       Division of Biological Sciences
                     University of California, San Diego
                           johnh@biomail.ucsd.edu

              Distributed under the GNU General Public License

               Type "help" or "help " for information
                     on the commands that are available.


MrBayes >

As a Non-Interactive Batch Process

sh UNIX Shell Command Example non-interactive usage of mb 
[mikewong @ccls ~]$ export PREFIX=/home/mikewong/research/spicerlab/mrbayes

[mikewong @ccls ~]$ bsub -N -u mikewong@sfsu.edu \
> -o $PREFIX/xerula-lava.out \
> -e $PREFIX/xerula-lava.err \
> mb $PREFIX/Xerula.nex

A script has been written to simplify this process:

sh UNIX Shell Command Recommended non-interactive usage of mb 
[mikewong @ccls ~]$ lava-mb -u mikewong@sfsu.edu Xerula.nex

Using cluster-mb

More on this coming soon! (The cluster needs to be re-configured to support LAM again.)

Last revised: r1 - 18 Jul 2007 - 22:44:19 - Mike Wong
 
Center for Computing for Life Sciences
San Francisco State University
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