Install OpenBUGS

Steps

Download OpenBUGS (Note only OpenBUS 2.2.0 works on unix machines) and upload it to dscratch. First upload it to AFS and then copy it to dscratch.
Unzip the file on the cluster

Create a file called linbugs with the following content and change permission using chmod 755 lingbugs

#!/bin/bash

export LD_ASSUME_KERNEL=2.4.1

DIR=$(dirname $0)
cd "$DIR"
if [ \! -e "$DIR/temp" ] ; then
        mkdir "$DIR/temp"
fi

if [ -e bugs.so ] ; then
        ./cbugs "$DIR" "$DIR/temp" "/bugs.so"
else
        ./cbugs "$DIR" "$DIR/temp" "/brugs.so"
fi

Create a file called Cbugs and compile it using

  gcc -o cbugs CBugs.c -ldl -m32

. The file includes the following codes

/*              GNU General Public Licence

        This small C program loads the bugs.so ELF shared library. 
        Save it as a .c file and then
        compile it on Linux using gcc -o cbugs Cbugs.c -ldl

*/

#include <dlfcn.h>
#include <stdio.h>
#include <string.h>

int main (int argc, char **argv)
{
        void * handle;

        handle = dlopen("./bugs.so", RTLD_LAZY);
        if (handle)
        {
                dlclose(handle);
        }
        return 0;
}

An example

Start OpenBUGS by
```
./linbugs
```
in the OpenBUGS directory

If OpenBUGS successfully run, you will see

OpenBUGS ClassicBUGS release 2.1.1
type 'modelQuit()' to quit
Bugs>

Then type in the following commands (those after >)

 Bugs> modelCheck("Examples/Airmodel.txt")
model is syntactically correct
Bugs> modelData("Examples/Airdata.txt")
data loaded
Bugs> modelCompile()
model compiled
Bugs> modelInits("Examples/Airinits.txt")
model is initialized
Bugs> modelUpdate(100000)
100000 updates took 4 s
Bugs> samplesSet("theta")
monitor set
Bugs> summarySet("theta")
monitor set
Bugs> modelUpdate(10000)
10000 updates took 0 s
Bugs> samplesStats("theta")
                         mean      sd        MC_error  val2.5pc  median    val97.5pc start     sample
theta[1]                 -1.1      1.332     0.1092    -5.243    -0.7288   0.2504    101001    10000
theta[2]                 0.05332   0.05231   0.004327  0.002579  0.03949   0.2046    101001    10000
Bugs> samplesCoda("*","output")
CODA files written
Bugs> modelQuit()

Useful links

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Table of Contents

Install OpenBUGS

Steps

An example

Useful links