MrBayes on the Cluster
3.1 is installed on the cluster and is compiled to run
in parallel. The MrBayes 3.1 manual can be downloaded
1. Prepare your nexus data file. It is important that
this file has UNIX line breaks (use TextWranger) and that
this file has a ".nexus" extension. Note also that
MrBayes does not support all of the characters recognized
by PAUP - see page 10 of the MrBayes
manual for details.
2. Append a MrBayes block to your nexus file. An example
is provided below. You may (must) want to change some of
the parameter options to suit your specific needs (e.g.,
lset, ngen, burnin, nruns, nchains, filename) - read the
MrBayes manual if you have a question about one of
settings in the block. Running an analysis with this
block will run three independent runs each using 4
If you want to remove the first 25% of the trees as burnin, add the following line to the MrBayes block:
relburnin = yes burninfrac = 0.25
This is also the default if you ask Mesquite to write a MrBayes block for you.
- BEGIN mrbayes;
prset [place your model parameters here];
lset [place your model parameters here];
mcmcp nruns=3 ngen=10000000 printfreq=1000
samplefreq=500 nchains=4 savebrlens=yes
3. Use sftp to upload your data file into an empty
directory (use Fugu).
4. Log on to the cluster and change into the directory
with your nexus data file.
5. To prepare for your run type
6. To run your job type "runjobs.mrbayes 1 1". By
default MrBayes will use 4 processors. To use more
processors type the number that you desire after the
second 1. For example to use 12 processors, type
"runjobs.mrbayes 1 1 12". If you typed this and used the
above block in your data file, you would run three
independent runs, each with 4 chains, and with each chain
using using its own processor. Note that the number of
chains must be at least as great as the number of
processors. Also note that when running Bayes jobs on
the cluster a run is seen as one job regardless of the
number of processors being used. Normally one is
automatically limited to 32 processors, but this can be
exceeded when using MrBayes. Please be considerate and do
not exceed 32 processors.
7. Your .t and .p files for each run will
be output into the same directory that contains your
input nexus file. To check the status of a run type
See the U.M.-St. Louis MrBayes
page for further options on running MrBayes.