AW: AW: [GE users] Export Env Variables

jcold jc at axyzfx.com
Wed Sep 23 21:15:18 BST 2009


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I've been having a lot of problems with this too - I can't seem to submit a 
task that has any spaces in it(!) such as 'ls -l'.  'ls' on it's own, 
however, works fine with <exec "$@"> as the starter script.  Could this be 
because the default script we're using is actually csh, not bash?  I get an 
error like this:

	/SGE/bin/lx24-amd64/starter_mask.sh: line 5: exec: ls -l: not found

	Also, the entire point of the exercise is to get SGE to have better 
permissions on it's out files, but even just running 'ls' as a job, which 
works fine, the output file doesn't have any different permissions, despite 
the fact I set 'umask 000' in the starter script.

	Cheers,

	J.C.

On Friday 18 September 2009 11:40, carsten wrote:
> I tried the following calls:
>
> exec "$@"
>
> exec "$*"
>
> exec $SGE_STARTER_SHELL_PATH "$*"
>
> exec $SGE_STARTER_SHELL_PATH "$@"
>
>
>
> All of them did not work. The application starts, but the setup of the MPI
> universe timed out. Other MPI implementations have no problems, but this is
> the only PE we have that uses catch_rsh. Setting the starter_method back to
> NONE, the application works well.
>
> -- Carsten
>
>
> -----Ursprüngliche Nachricht-----
> Von: reuti [mailto:reuti at staff.uni-marburg.de]
> Gesendet: Freitag, 18. September 2009 16:13
> An: users at gridengine.sunsource.net
> Betreff: Re: AW: [GE users] Export Env Variables
>
> Am 18.09.2009 um 15:42 schrieb carsten:
> > Replacing the starter_method seems to be the only way.
> >
> > The problem is, that a simple replacement with 'exec "$@" ' crashes
> > a PE that use catch_rsh (was the case in 6u10, have not tested with
> > a 6.2 version yet).
>
> AFAIK the starter_method is (and was) never used for the PE scripts.
> Only for the jobscript.
>
> It will be applied for the slave tasks though, but this shouldn't be
> a problem. Maybe it depends on the kind of parallel lib. E.g. with
> MPICH(1) I see no problem.
>
> Did you use "$*" instead?
>
> -- Reuti
>
> > Regards,
> > Carsten
> >
> >
> > -----Ursprüngliche Nachricht-----
> > Von: reuti [mailto:reuti at staff.uni-marburg.de]
> > Gesendet: Freitag, 18. September 2009 15:01
> > An: users at gridengine.sunsource.net
> > Betreff: Re: [GE users] Export Env Variables
> >
> > Am 18.09.2009 um 14:42 schrieb matbradford:
> >> Is it possible to export environment variables from the PE start
> >> script so that they are accessible by the job.
> >
> > No.
> >
> >> We have an OpenMPI job and are currently using linux modules to
> >> load the environment correctly .
> >>
> >> At the moment this is in the actual job submission script, but we
> >> would prefer to move it to the PE start up script.
> >>
> >> I?ve had a quick play, and it doesn?t seem to matter what I do, I
> >> can?t create an environment variable of any sort in the PE start
> >> script and then access it from within the job.
> >>
> >> Any thoughts would be much appreciated.
> >
> > You can user a starter_method in the definition of the queue and then
> > exec the program:
> >
> > #!/bin/sh
> > export blabla=fubar
> > exec "$@"
> >
> > -- Reuti
> >
> >> Cheers,
> >>
> >> Mat
> >>
> >> Matthew Bradford
> >>
> >> Information Specialist
> >>
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