[GE users] PATH problem

Bradford, Matthew matthew.bradford at eds.com
Tue Aug 15 21:30:37 BST 2006


Reuti,

Thanks for your advice.

I was setting the path in the users environment at submission time, but
had to change two things to get it working 100% of the time. 

Firstly,  I changed the queue configuration to use /bin/csh and
posix_compliant, it had been set to /bin/bash and unix_behaviour.
Secondly, I added the -V flag to pass in the user's environment.  I'm
not sure that I understand the effects of the posix_compliant or
unix_behaviour flags, but as long as it works that'll do for now.

Cheers,

Mat
-----Original Message-----
From: Reuti [mailto:reuti at staff.uni-marburg.de] 
Sent: 08 August 2006 10:12
To: users at gridengine.sunsource.net
Subject: Re: [GE users] PATH problem

Am 08.08.2006 um 10:50 schrieb Bradford, Matthew:

> We have installed grid engine portal to allow submission to a cluster,

> but we are having a slight problem.
>
> It seems that when a job is submitted via the portal, a subsequent 
> "qacct" job is also submitted to return info to the portal. This is 
> the part we are having problems with.
>
> The section of the script that is causing the problem is listed below:
> __________
> #!/bin/sh
> qacct -j 950
> _________
>
> I have created this as a separate script to isolate the problem rather

> than part of the portal generated script. I then simply submit this 
> script to our cluster using qsub.
>
> If I put a which qacct  into this script, then I get the following
> output:
>
> "which: no qacct in (/tmp/<jobid>.serial.q:/usr/local/bin:/bin:/usr/
> bin)"
> /usr/local/sge6.0/default/spool/comp00/job_scripts/<jobid>: line 4:  
> qacct: command not found.
You have to source the settings.sh file to add the location of the SGE
installation to your $PATH. This you can try to put in a .bashrc or
directly into you script, i.e.:

. /usr/sge/default/common/settings.sh

(or you can try to use $SGE_ROOT there, instead of the full path)

-- Reuti

> If I dump the environment at this point, then the PATH is set to
>
>         /tmp/<jobid>.serial.q:/usr/local/bin:/bin:/usr/bin
>
> The SGE_O_PATH is set to the user's full path.
>
> If I submit the same script to an alternative cluster, then everything

> seems to work, and the PATH appears to be set to the full path as 
> specified in their .login script.
>
>
> Am I missing something?
>
> Any help would be much appreciated.
>
> Cheers,
>
> Mat
>
> Mat Bradford
>
>

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