Sun Gridengine TSI: Losing PATH

[Aaron Hicks]

Hi,

I've got Unicore working over our Rocks cluster via the Sun Grid engine TSI.

This works fine for 'trivial' scripts, but the SGE-TSI is modifying some environment variables, the path in particular.

The path ends up trimmed down to:
PATH=/tmp/51.1.all.q:/usr/local/bin:/bin:/usr/bin

I've tried editing the path set in /opt/unicore/tsi/tsi_sun_gridengine/tsi by modifying the line:

$ENV{PATH}="/usr/bin";

This does not seem to be an issue with the SGE itself as when sending scripts from the command line using qsub, everything works as it should and the PATH variable is normal.

Once I crack this, I'll be trying to make this go multi-user.

There aren't really any log file here, as the problem is clearly a path issue when SDERR comes back with "input: line 4: java: command not found".

Regards,

Aaron Hicks

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[Bernd Schuller]

hi Aaron,

in SGE you can export environment variables using the "-v" option to
qsub, so it should be possible to modify the submit command in Submit.pm
and export the PATH variable. In Submit.pm this is the line

 my $command = "$main::submit_cmd ......

which could be changed to

 my $command = "$main::submit_cmd -v PATH ......

The value can also be defined there, else the value from the "tsi" file
should be used (can't test this unfortunately, since I don't have an SGE
installation available)

Best regards,
Bernd.

PS: my reference for the qsub options was:
<http://gridengine.sunsource.net/nonav/source/browse/~checkout~/gridengine/doc/htmlman/manuals.html?pathrev=V62u3_TAG>

On Fr, 2009-08-21 at 05:54 +0200, Aaron Hicks wrote:

> Hi,
>
> I've got Unicore working over our Rocks cluster via the Sun Grid engine TSI.
>
> This works fine for 'trivial' scripts, but the SGE-TSI is modifying some environment variables, the path in particular.
>
> The path ends up trimmed down to:
> PATH=/tmp/51.1.all.q:/usr/local/bin:/bin:/usr/bin
>
> I've tried editing the path set in /opt/unicore/tsi/tsi_sun_gridengine/tsi by modifying the line:
>
> $ENV{PATH}="/usr/bin";
>
> This does not seem to be an issue with the SGE itself as when sending scripts from the command line using qsub, everything works as it should and the PATH variable is normal.
>
> Once I crack this, I'll be trying to make this go multi-user.
>
> There aren't really any log file here, as the problem is clearly a path issue when SDERR comes back with "input: line 4: java: command not found".
>
> Regards,
>
> Aaron Hicks
>
> Please consider the environment before printing this email
> Warning:  This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails.
> The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Unicore-support mailing list
> Unicore-support@...
> https://lists.sourceforge.net/lists/listinfo/unicore-support

--
Dr. Bernd Schuller
Distributed Systems and Grid Computing
Juelich Supercomputing Centre, http://www.fz-juelich.de/jsc
Phone: [phone] (fax -8556)
Personal blog: www.jroller.com/page/gridhaus


------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------

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trial. Simplify your report design, integration and deployment - and focus on
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_______________________________________________
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[Aaron Hicks]

Hi Bernd,

Thanks, that works nicely now.

Regards,

Aaron Hicks

> -----Original Message-----
> From: Bernd Schuller [mailto:b.schuller@...]
> Sent: Friday, 21 August 2009 6:24 p.m.
> To: Aaron Hicks
> Cc: unicore-support@...
> Subject: Re: [Unicore-support] Sun Gridengine TSI: Losing PATH
>
> hi Aaron,
>
> in SGE you can export environment variables using the "-v" option to
> qsub, so it should be possible to modify the submit command in
> Submit.pm
> and export the PATH variable. In Submit.pm this is the line
>
>  my $command = "$main::submit_cmd ......
>
> which could be changed to
>
>  my $command = "$main::submit_cmd -v PATH ......
>
> The value can also be defined there, else the value from the "tsi" file
> should be used (can't test this unfortunately, since I don't have an
> SGE
> installation available)
>
> Best regards,
> Bernd.
>
> PS: my reference for the qsub options was:
> <http://gridengine.sunsource.net/nonav/source/browse/~checkout~/grideng
> ine/doc/htmlman/manuals.html?pathrev=V62u3_TAG>
>
> On Fr, 2009-08-21 at 05:54 +0200, Aaron Hicks wrote:
> > Hi,
> >
> > I've got Unicore working over our Rocks cluster via the Sun Grid
> engine TSI.
> >
> > This works fine for 'trivial' scripts, but the SGE-TSI is modifying
> some environment variables, the path in particular.
> >
> > The path ends up trimmed down to:
> > PATH=/tmp/51.1.all.q:/usr/local/bin:/bin:/usr/bin
> >
> > I've tried editing the path set in
> /opt/unicore/tsi/tsi_sun_gridengine/tsi by modifying the line:
> >
> > $ENV{PATH}="/usr/bin";
> >
> > This does not seem to be an issue with the SGE itself as when sending
> scripts from the command line using qsub, everything works as it should
> and the PATH variable is normal.
> >
> > Once I crack this, I'll be trying to make this go multi-user.
> >
> > There aren't really any log file here, as the problem is clearly a
> path issue when SDERR comes back with "input: line 4: java: command not
> found".
> >
> > Regards,
> >
> > Aaron Hicks
> >
> > Please consider the environment before printing this email
> > Warning:  This electronic message together with any attachments is
> confidential. If you receive it in error: (i) you must not read, use,
> disclose, copy or retain it; (ii) please contact the sender immediately
> by reply email and then delete the emails.
> > The views expressed in this email may not be those of Landcare
> Research New Zealand Limited. http://www.landcareresearch.co.nz
> >
> > ---------------------------------------------------------------------
> ---------
> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> 30-Day
> > trial. Simplify your report design, integration and deployment - and
> focus on
> > what you do best, core application coding. Discover what's new with
> > Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> > _______________________________________________
> > Unicore-support mailing list
> > Unicore-support@...
> > https://lists.sourceforge.net/lists/listinfo/unicore-support
> --
> Dr. Bernd Schuller
> Distributed Systems and Grid Computing
> Juelich Supercomputing Centre, http://www.fz-juelich.de/jsc
> Phone: [phone] (fax -8556)
> Personal blog: www.jroller.com/page/gridhaus
>
>
> -----------------------------------------------------------------------
> -------------------------
> -----------------------------------------------------------------------
> -------------------------
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> -----------------------------------------------------------------------
> -------------------------
> -----------------------------------------------------------------------
> -------------------------

Please consider the environment before printing this email
Warning:  This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails.
The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

------------------------------------------------------------------------------
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trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
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