[GE users] PATH problems with grid engine 6

Brady Catherman bradyc at uidaho.edu
Fri Nov 18 00:04:26 GMT 2005


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Oh sweet =) I haven't even had time to look. We have the entire  
cluster full of jobs so there is no room for testing yet. I will have  
to wait for the holiday break before I can tweak with anything =)




On Nov 17, 2005, at 3:46 PM, Reuti wrote:

> 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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>>>>>>>> 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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