[GE users] Scheduling Questions

Reuti reuti at staff.uni-marburg.de
Thu Dec 15 18:29:34 GMT 2005


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Hi,

Am 15.12.2005 um 18:02 schrieb Raymond Chan:

> Hi all,
>
>
>
> I know this has been asked before in some way or another, and I?m  
> sorry if this is a repeat.  I?m not sure where to begin because as  
> I look through the list there are things that may or may not apply,  
> so I?ll be more direct and just ask.  Thanks to anyone in advance  
> who can help, and again I apologize if this was answered recently:
>
>
>
> I have a total of 6 dual cpu nodes that I am submitting parallel  
> mpich & pvm jobs (qsub ?pe 6) as well as regular non-parallel jobs  
> to.   As you know, some jobs take longer than others to complete,  
> so if job #1 is a job that will take 5 hours to complete, and job  
> #2 will take only 5 minutes, is there a way to automatically in SGE  
> make certain jobs jump in queue over jobs that are running a long  
> time so these smaller jobs can finish (sort of in a round robin  
> sort of way where each job maybe gets a certain amount of time  
> before switching)?  More clearly, a large job #1 holds up the queue  
> and everyone behind it is stuck, so what?s the best approach at  
> solving this sort of scheduling problem?
>
>
>
> I?m trying to run a department website at a university where  
> professors will be able to submit SGE jobs via the web for  
> bioinformatics apps that can take a long time.  It?d be nice if I  
> had a good way of allowing each professor to get a fair share of  
> the cluster instead of one guy holding up the whole thing.  Would  
> it also be possible to allow SGE to run two jobs at once on the  
> queue rather than one (or would this not be a good or possible  
> approach)?
>
>
>
> Thanks again to anyone who can offer advice w/ these newbie  
> questions.  I?ve currently just been able to do jobs one at a time  
> nicely on my web system with everyone waiting behind that one job  
> to finish, but I need a nice scheduling method, and I have no idea  
> how to configure this in SGE.
how many short jobs are waiting there - is it always full? Depending  
on the amount of available memory, you can try a setup like we have  
here:

- one queue for long running jobs with a queue priority (i.e. nice  
value) of 19
- one queue for short running jobs (h_rt limited to some minutes)  
with a queue priority of 0

The nice values are only relatively in Linux, but this will give  
around 10% to 90% computing time between the queues. If there are no  
short jobs, e.g. during nights and weekends, the long running jobs  
gets the full CPU time anyway.


Seems in original you are looking for  feature like: after a maximum  
of two hours the jobs will be checkpointed and put at the end of the  
list of pending jobs again. So long running jobs wlll do their work  
in pieces of two hours.

-- Reuti
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