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):
--- 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 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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Hewson Sent: Thursday, April 24, 2008 9:45 AM To: 'R-help@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: [EMAIL PROTECTED] web: http://www.plymouth.ac.uk/staff/phewson -=-=-=-=-=-=-=-=-=-=-=-= ______________________________________________ R-help@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@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.
