====== Install OpenBUGS ======
===== Steps =====
  - Download [[http://mathstat.helsinki.fi/openbugs/OldBUGS/OpenBUGS220.zip|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 <code>

#!/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</code>
  - Create a file called Cbugs and compile it using <code>  gcc -o cbugs CBugs.c -ldl -m32 </code>. The file includes the following codes <code>
/*              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;
}
</code>

===== An example =====
  - Start OpenBUGS by <code>./linbugs</code> in the OpenBUGS directory
  - If OpenBUGS successfully run, you will see <code>OpenBUGS ClassicBUGS release 2.1.1
type 'modelQuit()' to quit
Bugs> 
</code> 
  - Then type in the following commands (those after >) <code> 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()

</code>

===== Useful links =====
  - http://web.maths.unsw.edu.au/~tduong/research/rlinbugs.html
  - http://web.maths.unsw.edu.au/~tduong/research/rlinbugs.html
  - http://www.hsph.harvard.edu/~paciorek/computingTips/R_code_calling_BUGS_in.html

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