lab:using_winbugs_on_the_notre_dame_clusters
Table of Contents
Steps
- Download OpenBUGS 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()