[R] R and condor

Scillieri, John John.Scillieri at constellation.com
Fri Apr 25 15:31:44 CEST 2008


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

--- CleanCondorLogs.condor -----------------------

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:

------- Run.R.bat --------------

C:\windows\system32\net.exe use H: <NETWORK PATH TO H: DRIVE USED BY
"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: 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


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

email: paul.hewson at plymouth.ac.uk
web: http://www.plymouth.ac.uk/staff/phewson

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