[GE users] PATH problems with grid engine 6

Brady Catherman bradyc at uidaho.edu
Thu Nov 17 23:28:18 GMT 2005


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Oh man thats just awesome =)

Thanks for helping man it works great now!  Now I just need to figure  
out how to do it on our Apple cluster.. (Stinking qmon doesn't work  
right so everything is done through qconf)





On Nov 17, 2005, at 3:06 PM, Reuti wrote:

> Am 17.11.2005 um 22:54 schrieb Brady Catherman:
>
>> In my test script I can get it working. I am trying to do this  
>> before control is handed over to the users script.
>
> Okay, then you have to use a script, which is the starter_method,  
> like in the thread I mentioned:
>
> #!/bin/sh
> . ~/.bash_profile
> exec $*
>
> put this script e.g. in a created folder $SGE_ROOT/tools, make it  
> executable, and specify it as starter_method in the queue. This  
> way, instead of the default behavior to start a shell with the  
> users script, it's the responibility of the starter_method to do  
> it. Details you can find in the man page of queue_conf.
>
> Cheers - Reuti
>
>>
>>
>>
>> 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?
>>>>>>
>>>>>> ----------------------------------------------------------------- 
>>>>>> ----
>>>>>> To unsubscribe, e-mail: users- 
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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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>>>
>>
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