Linbugs ( aka Openbugs or Winbugs)
From HPC
You can run your Winbugs\Openbugs work on the HPC cluster using Linbugs which is the classic interface version and can be used from a terminal.
Contents |
Opening Linbugs
linbugs
Issues and Problems
The only issue know with the linux version is the command modelSaveLog('log.txt') cause the an error. This command should not be used, you will find that a file called run.out is create automatically which is the same as the log.
Example
Create the following files
data.txt
list( t = c( 9.43000E+01, 1.57000E+01, 6.29000E+01, 1.26000E+02, 5.24000E+00, 3.14000E+01, 1.05000E+00, 1.05000E+00, 2.10000E+00, 1.05000E+01 ), x = c( 5, 1, 5, 14, 3, 19, 1, 1, 4, 22 ), N = 10 )
model.txt
model
{ for (i in 1 : N) { theta[i] ~ dgamma(alpha, beta) lambda[i] <- theta[i] * t[i] x[i] ~ dpois(lambda[i]) } alpha ~ dexp(1) beta ~ dgamma(0.1, 1.0) }
init1.txt
list( alpha = 1.00000E+00, beta = 1.00000E+00 )
Now open linbugs
linbugs
and enter the following commands (note, this script could be saved as a text file and run via the command 'linbugs < script.txt')
modelCheck('model.txt') modelData('data.txt') modelCompile(1) modelInits('init1.txt', 1) modelGenInits() samplesBeg(501) modelSetRN(314159) modelUpdate(500, 1) samplesSet(theta) samplesSet(alpha) samplesSet(beta) samplesSet(deviance) modelUpdate(500, 1) samplesStats('*') samplesCoda('*', 'coda') modelQuit()
This will have create the following CODA files
codaCODAindex.txt codaCODAchain1.txt