Re: [R] R and condor

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

Paul,

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:\windows\system32\net.exe use H: <NETWORK PATH TO H: DRIVE USED BY YOUR CONDOR/R PROGRAM> /PERSISTENT:NO
"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.

John

-----Original Message-----
From: r-help-bounces_at_r-project.org [mailto:r-help-bounces_at_r-project.org] On Behalf Of Paul Hewson
Sent: Thursday, April 24, 2008 9:45 AM
To: 'R-help_at_r-project.org'
Subject: [R] R and condor

Hello,

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
Queue

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

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

Best

Paul

-=-=-=-=-=-=-=-=-=-=-=-=
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

email: paul.hewson_at_plymouth.ac.uk
web: http://www.plymouth.ac.uk/staff/phewson -=-=-=-=-=-=-=-=-=-=-=-=



R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. >>> This e-mail and any attachments are confidential, may contain legal, professional or other privileged information, and are intended solely for the addressee. If you are not the intended recipient, do not use the information in this e-mail in any way, delete this e-mail and notify the sender. CEG-IP1

R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Fri 25 Apr 2008 - 13:49:32 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Fri 25 Apr 2008 - 14:30:32 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive