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Re: [Condor-users] R and condor



Paul,
The command line args for R are a bit obscure. To get started, write
your job as a small dos batch file and get it running on your machine.
Then worry about running it on condor. Your batch file will be something
like (use % substitutions later) 
---
"C:\Program Files\R\R-2.5.1\bin\Rterm.exe" --slave --vanilla < test0.R
--
This should run from the command line.

Next tell condor about it:
---
Universe = vanilla
Executable = test0.bat
transfer_input_files = test0.R 
Error = test0.err 
Output = test0.out
Log = test0.log
Queue
--

You should see some progress now..
P


-----Original Message-----
From: condor-users-bounces@xxxxxxxxxxx
[mailto:condor-users-bounces@xxxxxxxxxxx] On Behalf Of Paul Hewson
Sent: Friday, 25 April 2008 4:37 PM
To: condor-users@xxxxxxxxxxx
Subject: [Condor-users] R and condor

Hello,
(I've already posted this on the R-help list, apologies for
cross-posting)

I would be extremely grateful if anyone is able to provide any (rather
obscure) advice on using R with Condor.    Essentially, it seems
possible here to use condor with stand alone executables, but I'm
getting stuck trying to submit batch jobs which software on the target
machine.

 think I'm following  instructions (Xianhong Xie,R News 5(2) 13-15
http://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdf) 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@xxxxxxxxxxxxxx
web: http://www.plymouth.ac.uk/staff/phewson
-=-=-=-=-=-=-=-=-=-=-=-=

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