OpenBUGS

Description

From the OpenBUGS website: BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. The user specifies a statistical model, of (almost) arbitrary complexity, by simply stating the relationships between related variables. The software includes an ‘expert system’, which determines an appropriate MCMC (Markov chain Monte Carlo) scheme (based on the Gibbs sampler) for analysing the specified model. The user then controls the execution of the scheme and is free to choose from a wide range of output types.

Version

  • 3.2.2

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

OpenBUGS requires the following module file to run:

  • apps/openbugs/3.2.2

Running OpenBUGS on CIRCE/SC

The OpenBUGS user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

If, for example, you have your OpenBUGS inputs in your /work directory, you would change to that directory and create a submit script like this:

  • The script below (for testing, name it “openbugs-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.
#!/bin/bash
#
#SBATCH --comment=openbugs-test
#SBATCH --ntasks=8
#SBATCH --job-name=openbugs-test
#SBATCH --output=output.%j.openbugs-test
#SBATCH --time=01:00:00

#### SLURM 8 processor OpenBUGS test to run for 1 hour.

module purge
module load apps/openbugs/3.2.2

mpirun OpenBUGS 

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./openbugs-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with OpenBUGS to the IT Help Desk: rc-help@usf.edu