Re: [HTCondor-users] Problems with Condor & R

["O'Donnell, Michael" <odonnellm@xxxxxxxx>]

One thing that I do is store the R install folder on a centralized storage device and then using UNC paths I point to the R executable, script, and arguments I need. Since we are using Windows machines that generally have users on them, an install of R on a file server allows me to more easily control libraries and versions for projects that I use with HTCondor.

For example a batch that Condor would run would look something like this:

UNC\Apps\R\R-2.12.2\bin\i386\Rterm.exe myRCommands.R Args

Maybe something like this will work for you. I believe I found in the past that using UNC paths for the Executable in the submit file does not work (would need to look at notes again), but you could create a batch that calls R.

mike

On Tue, Jun 11, 2013 at 1:14 PM, Morway, Eric <emorway@xxxxxxxx> wrote:

After witnessing firsthand the power of Condor (about a year ago), I was instantly sold.  So, for the last several months we've been trying to get condor set up on about 25 machines (with more slated for the future).  I have a test simulation that we've been using to test it out and here is what it consists of:  

1) Call a python script that pre-processes some model input file

2) Call the process model (MT3DMS)

3) Call an R script that post-processes MT3DMS output.

Everything runs great except R, which I've determined from reading the log file generated by Condor.  I've tried invoking R in two different ways.  The first way was to put the directory with Rscript.exe on the path and call the R script like this:

Rscript.exe myRCommands.R

The second approach included a copy of the R directory generated during its installation in the zip file distributed by Condor.  I then set a relative path in the batch file that runs the model like so:

..\R-3.0.0\bin\Rscript.exe myRCommands.R

Both approaches seem to work fine when I manually pull-down a copy of the zip file on one of the 25 machines running condor, unzip it, and execute the batchfile contained therein.  However, trying to get Condor to run it has consistently led nowhere.  The error message in the log file reflects the fact that R wasn't run:

" Problem encountered:-

 ------------------------------------------------------------------------------

 Cannot open model output file UnsatZnCDF_output.txt.

 ------------------------------------------------------------------------------"

The file, "UnsatZnCDF_output.txt", will be generated by R.  Why, when I run the contents of the zip file manually, do things seem to work OK, but with condor R is seemingly no called?  Where do I begin to investigate if there are permission issues?  

Respectfully,

Eric

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