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OpenBUGS on Biowulf
BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. All current development is focused on the open-source version, called OpenBUGS.

OpenBUGS has a GUI interface which can be used on Helix if desired. The most appropriate way to use it on Biowulf are the OpenBUGS scripting commands. These are similar to the R interface to OpenBUGS called BRugs.

To make use of the scripting commands, a minimum of three files is required: a file containing the script commands, a file containing the BUGS language representation of the model; and a file (or several) containing the data. If initial values are supplied (recommended) rather than generated by OpenBUGS, an additional file is required for each chain.

How to run a single OpenBUGS batch job

Set up a batch file along the following lines:
(the sample OpenBUGS commands below are taken from the Rats example in the manual.

Note that the openbugs module must first be loaded to set up the environment, with 'module load OpenBUGS'.

#!/bin/bash
#  --------  this file is called mybugs.bat-------------------------
#PBS -N OpenBUGS

# send email when job starts and ends
#PBS -m be       

# send standard error and standard output to a single file
#PBS -j oe       

module load OpenBUGS                       #sets up paths for OpenBUGS

OpenBUGS << EOF 
modelCheck('/data/user/mydir/Ratsmodel.txt')
modelData('/data/user/mydir/Ratsdata.txt')
modelCompile(1)
modelInits('/data/user/mydir/Ratsinits.txt',1)
modelUpdate(1000)
samplesSet('alpha0')
samplesSet('beta.c')
samplesSet('sigma')
modelUpdate(10000)
samplesStats('*')
EOF

Submit this job with

qsub -l nodes=1 mybugs.bat

The output from this run will appear in the standard output file for the job, called OpenBUGS.o#######, where ####### is the job number.

Documentation

OpenBUGS User Manual
Scripts in OpenBUGS