[GE users] PATH problems with grid engine 6

Reuti reuti at staff.uni-marburg.de
Thu Nov 17 23:46:14 GMT 2005


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Am 18.11.2005 um 00:28 schrieb Brady Catherman:

> 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)

For adjusting a queue it's just "qconf -mq <qname>" which will open a  
vi session, where you'll find the entry starter_method. - Reuti

>
>
>
>
> 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?
>>>>>>>
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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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>>>> help at gridengine.sunsource.net
>>>>
>>>
>>>
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