[R] Running R-program as queue jobs

[Peter Dalgaard]

Jason Turner <jasont at indigoindustrial.co.nz> writes:

> Philipp Pagel wrote:
> > 	Hi!
> > On Thu, Nov 13, 2003 at 09:59:48AM +0000, Arne Gjuvsland wrote:
> >
> >>I have a problem with running my R programs as queue jobs. When I try
> >>to submit a batch file to the queue with qsub I get the following error
> >>message:
> >>____________________________________________________________
> >>
> >>/home/gjuvslan/kluster/R-1.7.1/bin/R.bin: error while loading shared
> >> libraries: libpcre.so.0: cannot load shared object file: No such
> >> file or directory
> >>____________________________________________________________
> >>
> >>When executed from the command prompt the batch file does its job.
> > Did you run the script on the same machine in both cases? I got
> > burnt a
> > couple of times with different machines running different versions of
> > the OS, non-identical versions of shared libraries etc...
> >
> 
> In addition to Philipp's good sugestion, I've been burnt on the same
> machine, but with the batch job running as a different user.  When
> environment variables are needed, or private libraries need to be
> loaded, things go bad very quickly.

Also, environment variables may be set differently between interactive
and batch shells. E.g. my crontab file looks like this

CVS_RSH=ssh
35 0 * * *  $HOME/scripts/r-bugs-commit > /dev/null
...

for a reason. In Arne's case, I'd suspect the setting of
LD_LIBRARY_PATH. 

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
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~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907