[GE users] qsub and holding while a job is *executing*?

jgrn307 greenberg at ucdavis.edu
Thu Jan 7 19:08:14 GMT 2010


Excellent, looks like the consumable resources is what I'm after (for 
one phase, GRASS has to run in a single directory, hence the race 
condition problem -- it seems all I do is set the number of resources 
for "grass" to equal 1) -- are resources something that users are 
allowed to define (as opposed to the grid engine admin)?  I'm currently 
testing the algorithm out on my personal machine, so I can hack at qmon 
to my heart's extent, but I was hoping to make sure I wrote the 
algorithm such that it could be deployed on any grid engine system where 
I may not be an admin -- how do I go about defining a consumable 
resource at the command line and then removing it later?  I see how to 
request the resource in that example.  Thanks again!

--j

reuti wrote:
> Hi,
>
> Am 07.01.2010 um 10:14 schrieb jgrn307:
>
>   
>> Grid-engineers:
>>
>>    I'm a total noob to grid engine, so I apologize if this is a  
>> ridiculously simple question: I have a situation where I need to  
>> hold a job if and ONLY if a job with some name patterns is  
>> currently *running*, not if it has finished executing.  This is due  
>> to an unfortunate situation which rises during a certain phase of  
>> my parallel project where it must enter a specific program (GRASS  
>> GIS, in my case) that does NOT allow concurrent access, e.g. two  
>> jobs cannot access the program at the same time (the program is not  
>> thread-safe).
>>     
>
> when you run a second instance of the program, it should be  
> independent from each other. Maybe you have to instruct the program  
> to use a special temporary directory or so. The usual one created by  
> SGE for each job is $TMPDIR, and maybe it's necessary to `export TMP= 
> $TMPDIR` or similar.
>
>
>   
>>   So in the situation where I have 3 jobs: job01, job02, job03; how  
>> do I qsub these so this situation is upheld (a job will not execute  
>> unless NONE of the other
>> jobs is running).  My understanding is that -hold-jid is designed  
>> for process dependencies and checks for job completion (e.g. job02  
>> can't start until job01), so this isn't what I want, at least I  
>> don't think it is.  Any help you give me would be much appreciated,  
>> thanks!
>>     
>
> Nevertheless, you can create a custom complex with an amount of one  
> (similar to managing it as a license count) and request for each of  
> your jobs of this type `... -l grass=1 ...`.
>
> http://wikis.sun.com/display/gridengine62u5/Example+1+-+Floating 
> +Software+License+Management
>
> -- Reuti
>
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-- 

Jonathan A. Greenberg, PhD
Postdoctoral Scholar
Center for Spatial Technologies and Remote Sensing (CSTARS)
University of California, Davis
One Shields Avenue
The Barn, Room 250N
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307

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