Install OpenBUGS 3.0.7 on Linux server

The following instructions were tested on Red Hat Enterprise Linux Server release 5.4 (Tikanga), Kernel version 2.6.18-164.11.1.el5. Could work for other linux releases.

The new version of OpenBUGS (v.3.0.7) can be run on Linux machine very easily. To install it on a linux machine, following these steps (adapted from openbugs.info)

• Create a directory named OpenBUGS307 and create two sub-directories within it: bin and lib.
• Download the shared library libOpenBUGS.so to the lib directory.
• Download the bash shell script, OpenBUGS, to the bin directory.
• Download the compiled C program, OpenBUGSCli to the bin directory.
• Change the permission of OpenBUGS and OpenBUGSCli using

  chmod 755 OpenBUGS OpenBUGSCli

To use the interactive OpenBUGS, in the prompt, type the following and return (in the folder of bin)

./OpenBUGS

Below is an example to run OpenBUGS interactively using the Rats example:

$ ./OpenBUGS
OpenBUGS version 3.0.7 rev 397
type 'modelQuit()' to quit
OpenBUGS> modelCheck("model.txt")
model is syntactically correct
OpenBUGS> modelData("data.txt")
data loaded
OpenBUGS> modelCompile()
model compiled
OpenBUGS> modelInits("init.txt")
model is initialized
OpenBUGS> modelUpdate(1000)
1000 updates took 0 s
OpenBUGS> samplesSet("alpha0")
monitor set
OpenBUGS> samplesSet("beta.c")
monitor set
OpenBUGS> samplesSet("sigma")
monitor set
OpenBUGS> modelUpdate(10000)
10000 updates took 0 s
OpenBUGS> samplesStats("alpha0")
                         mean      sd        MC_error  val2.5pc  median    val97.5pc start     sample
 alpha0                  106.6     3.669     0.04221   99.41     106.6     113.6     1001      10000
OpenBUGS> samplesStats("*")
                         mean      sd        MC_error  val2.5pc  median    val97.5pc start     sample
 alpha0                  106.6     3.669     0.04221   99.41     106.6     113.6     1001      10000
 beta.c                  6.186     0.1091    0.001411  5.972     6.187     6.398     1001      10000
 sigma                   6.097     0.468     0.007489  5.263     6.07      7.106     1001      10000
OpenBUGS> samplesCoda('*', 'codafilename')
OpenBUGS> modelQuit()

To run OpenBUGS in batch format, one can save all the scripts in a file such as script.txt and then issue the command at the prompt

./OpenBUGS script.txt

Instructions for executing OpenBUGS can be obtained by typing

./OpenBUGS -h

Below is a list of related files used in the example

• model.txt
• init.txt
• data.txt
• script.txt