[GE users] PATH problems with grid engine 6

Reuti reuti at staff.uni-marburg.de
Thu Nov 17 23:06:33 GMT 2005


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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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>
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