Re: [R] R and condor

From: Scillieri, John <>
Date: Fri, 25 Apr 2008 09:31:44 -0400


This is what some of our condor files look like. The script actually goes through and cleans out our log directory (hence the name):

JobName = CleanCondorLogs

LogHeader = $(JobName).$(Cluster).$(Process).$$(Machine)

input = <path to r script>/CleanCondorLogs.R output = <log directory here>$(LogHeader).out Error = <log directory here>$(LogHeader).err log = <log directory here>/CleanCondorLogs.log

executable = $ENV(SystemRoot)\system32\cmd.exe arguments = /Q /C RunR.bat

transfer_executable = False
should_transfer_files = No
getenv = True
environment = "TMP=C:\temp TEMP=C:\temp" run_as_owner = true
Universe = vanilla

The RunR.bat file looks like this:

"C:\R\R-2.6.1\bin\Rscript.exe" --no-save --no-restore --no-init-file --no-environ -

We use the Run.R.bat file because it lets us not only mount required network drives in Condor, but also upgrade our R as we see fit without having to change 100+ condor files to point to the new path to R.

Hope that helps, let me know if you still run into trouble.


-----Original Message-----
From: [] On Behalf Of Paul Hewson
Sent: Thursday, April 24, 2008 9:45 AM
To: ''
Subject: [R] R and condor


I would be extremely grateful if anyone is able to provide any (rather obscure) advice on using R with Condor. I think I'm following Xianhong Xie's instructions (R News 5(2) 13-15) correctly, but my job just stays held in the queue (for days / months). I've checked condor_status to make sure there are plenty of machines available, but can't see any way to attack the problem of the non-running jobs.

I did wonder whether I should compile some small stand-alone executable to make sure that runs OK, but even then I'm not sure where I would go next. I have exhausted local advice on the matter.

For what it's worth, the condor script (and the even simpler R script) I'm working with at the moment are here:

Condor script file (submitted using condor_submit):

## condor script starts here:
Universe = vanilla
Executable = C:\Program Files\R\R-2.5.1\bin\Rterm.exe Getenv = true Arguments = vanilla Input = test0.R Error = test0.err Log = test0.log

Output = test.out

## R script file (test0.R)
pdf("test1.pdf", width = 6, height = 6)
plot(c(1:10), c(1:10))

I really would be grateful for any suggestions, hints, comments, sample working scripts etc.



Paul Hewson
Lecturer in Statistics
School of Mathematics and Statistics
University of Plymouth
Drake Circus
Plymouth PL4 8AA

tel (01752) 232778 (Campus)
tel (01752) 764437 (Tamar Science Park)
fax (01752) 232780

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