[torqueusers] help with unwanted concurrency in a torque script

Joshua Bernstein jbernstein at penguincomputing.com
Mon Dec 7 18:09:46 MST 2009


	I had another look at the script. It is interesting that CSH and BASH behave 
differently. Perhaps those commands depend upon some envar that is being handled 
differently between the two shells?

	My suggestion of job dependencies assumed the population and the analysis steps 
were in separate scripts. Perhaps you're submitting this script more then once 
and both are running at the same time?


Dan Kortschak wrote:
> Thanks for that. Though I'm still a little confused, since all the calls
> to scripts are in the same job script I'm not sure why later calls can
> start before previous ones have finished when this doesn't happen in a
> csh batch. But I will have a look.
> cheers
> Dan
> On Mon, 2009-12-07 at 16:57 -0800, Joshua Bernstein wrote:
>> Hey Dan,
>> 	What you are probably looking for is a feature called job dependencies. 
>> Basically you say that the reporting jobs are Dependant on the population 
>> script, and thus will not run until the population script completes.
>> http://www.clusterresources.com/torquedocs21/commands/qsub.shtml
>> Look towards the -W option to qsub:
>> $ qsub .... -W depend=...
>> In a nutshell the arguments to depend= are job identifiers. So you can submit 
>> the first populate job, and then every analysis gets submitted to depend on that 
>> job.
>> -Joshua Bernstein
>> Senior Software Engineer
>> Penguin Computing

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