[GE users] PATH problems with grid engine 6

Brady Catherman bradyc at uidaho.edu
Thu Nov 17 21:26:56 GMT 2005


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Our profile file is /etc/profile. That sources ~/.bash_profile.

I haven't been able to modify anything to get it working. Short of  
sourcing /etc/profile in my own submit script I can't get the path to  
change at all.

I am currently running with unix_behavior and /bin/bash --login as my  
shell settings. I think what I would really like to know is the  
process that SGE uses to start/stop processes.
For example, What I know about SGE now goes a little something like  
this:
Sge -> <PFM Device> -> Script

I am wondering if there is a clean and easy way to understand what  
the PFM Device is doing to get the environment up and running.

Anyways.. Im fairly new to SGE and I don't know of a good SGE manual  
(If you have one let me know)




On Nov 17, 2005, at 11:22 AM, Reuti wrote:

> Hi,
>
> Am 17.11.2005 um 19:33 schrieb Brady Catherman:
>
>> When we run scripts on our cluster SGE seems to screw up our local  
>> paths. We have programs in tons of different places and would  
>> prefer to not have locations hard coded.
>>
>> Hers is what I have tried:
>> 	Using unix_behavior with /bin/csh, /bin/tcsh and /bin/bash, /bin/ 
>> bash --login
>> 	Using posix_compliant with the same shells.
>> 	Using unix_behavior with a custom shell that sources /etc/profile.
>>
>> None of these seem to actually do anything though. The path is  
>> always "/tmp/492.1.all.q:/usr/local/bin:/usr/ucb:/bin:/usr/bin:"
>
> this is the default PATH for the jobs executed by SGE. To get your  
> custom PATH: where is it set by default: in /etc/profile.local,  
> your .bashrc, .bash_profile, .bash_login, .profile? If we know  
> this, we could simply source this. And this could be done in a  
> starter_method defined for the queues, so that the scripts stay  
> untouched.
>
> http://gridengine.sunsource.net/servlets/ReadMsg? 
> listName=users&msgNo=8503
>
> but using only one file at a time or a loop. I wonder, why "bin/ 
> bash --login" isn't working in your case.
>
> Cheers - Reuti
>
>> I had seen several solutions but they are always on the clients  
>> side of things. I would prefer to not have to force our clients to  
>> add stuff to scripts in order to get things working.
>>
>> Anybody know of a solution?
>>
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>
>
>
> --
> Philipps-University of Marburg
> AK Frenking / FB Chemie
> Thomas Reuter
> Hans-Meerweinstraße
> 35042 Marburg
> Germany
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> eMail reuti at staff.uni-marburg.de
>
>
>
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