[torqueusers] FW: Rpy

Brock Palen brockp at umich.edu
Mon Jun 4 06:16:44 MDT 2007


Try adding

#PBS -V  (capital V)

This will copy the environment from the submit node to the pbs  
environment.  We have to use this all the time because we use modules  
which messes with the environment.

modules.sf.net

Brock Palen
Center for Advanced Computing
brockp at umich.edu
(734)936-1985


On Jun 4, 2007, at 5:37 AM, Anthony Pemberton wrote:

> Dear Torque users,
>
> I got the following problem from one of my users. Does anyone have  
> experience of this type of problem?
>
> I tried running the test case on a quiet compute node to see if it  
> would work directly as the user did below on the admin node. There  
> appears to be a “PATH” error to the R command, but this is  
> difficult to trace in the qsub environment. Is there a way to  
> diagnose?
>
> Regards,
>
> Tony P.
>
> User query:
>
> Today I tried to submit some new jobs on the cluster.
> Everything works fine, excepting R/Rpy.
>
> When I use R in one of my jobs (python scripts) an error message
> appears.
> I don't get these errors when I run the scripts on the command line
> without subq.
>
> For example:
>
> When I start the python Console and I use the following code, no  
> errors.
> Also when I put this code in a python file and run this file without
> qsub (.py) no errors.
> -
> from rpy import *
> r.library('SparseM')
> -
>
> When I put this code in a python file and add it as a job it will give
> the following error:
> -
> Traceback (most recent call last):
>   File "testSP.py", line 1, in ?
>     import rpy
>   File "/usr/lib64/python2.3/site-packages/rpy.py", line 53, in ?
>     RVERSION = rpy_tools.get_R_VERSION(RHOME)
>   File "/usr/lib64/python2.3/site-packages/rpy_tools.py", line 98, in
> get_R_VERSION
>     raise RuntimeError("Couldn't execute the R interpreter" +
> RuntimeError: Couldn't execute the R interpreter `sh: R: command not
> found/bin/R'.
> -
>
> It looks like there is someting wrong with the Path to RPY?
>
> My Jobfile includes the following code:
> -
> #PBS -j oe
> cd  "$PBS_O_WORKDIR"
> python testSP.py > SP.out
> -
>
>
>
>
>
>
>
>
>
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