[GE users] PATH problems with grid engine 6

Brady Catherman bradyc at uidaho.edu
Thu Nov 17 21:54:22 GMT 2005


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In my test script I can get it working. I am trying to do this before  
control is handed over to the users script.




On Nov 17, 2005, at 1:44 PM, Reuti wrote:

> 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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>>>
>>>
>>>
>>> --
>>> 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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> To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
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