[GE users] PATH problems with grid engine 6

Reuti reuti at staff.uni-marburg.de
Thu Nov 17 21:44:41 GMT 2005


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Am 17.11.2005 um 22:26 schrieb Brady Catherman:

> 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.

If you source it (by ". ~/.bash_profile" in your script) it must  
change your path. Can you test with a little script like:

#!/bin/sh
echo $PATH
. ~/.bash_profile
echo $PATH

What is the output? If it's not working, what is in .bash_profile? In  
fact, often this leads to the elemination of the $TMPDIR in $PATH,  
which you might need to execute tightly integrated parallel jobs.

> 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

unix_behavior should stay in the queue definition, it's okay.

> 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)

Documentation is the original one from SUN: http:// 
gridengine.sunsource.net/documentation.html for SGE 6.0.

Cheers - Reuti

>
>
> 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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>>> To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
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>>
>>
>>
>> --
>> Philipps-University of Marburg
>> AK Frenking / FB Chemie
>> Thomas Reuter
>> Hans-Meerweinstraße
>> 35042 Marburg
>> Germany
>> FON +49-6421-28-25549
>> FAX +49-6421-28-25566
>> eMail reuti at staff.uni-marburg.de
>>
>>
>>
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>
>
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--
Philipps-University of Marburg
AK Frenking / FB Chemie
Thomas Reuter
Hans-Meerweinstraße
35042 Marburg
Germany
FON +49-6421-28-25549
FAX +49-6421-28-25566
eMail reuti at staff.uni-marburg.de



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