[IPython-User] Limitations (?) of ipython SGE support

Chris Filo Gorgolewski chris.gorgolewski@gmail....
Mon Jan 17 03:27:47 CST 2011


Thanks for your reply. It seems that interactive use is your main goal.
However, wouldn't out be better to submit every task separately using qsub
(instead of submitting ipengines)?

Thanks,
Chris
 On Jan 17, 2011 2:59 AM, "Brian Granger" <ellisonbg@gmail.com> wrote:
> Hi,
>
> On Thu, Jan 13, 2011 at 7:41 AM, Chris Filo Gorgolewski
> <chris.gorgolewski@gmail.com> wrote:
>> Hi,
>> I have recently played with ipython on our SGE cluster. I was
>> surprised to discover that ipython does not use qsub to submit every
>> job, but submits prespecified number of ipengines as jobs. Those I
>> presume run indefinitely and accept ipython tasks. This setup seem to
>> have two major drawbacks:
>
> Yes, this is a correct description of what happens.
>
>> 1) my cluster have nodes with different max job time. Depending what
>> you specify in the qsub option the job gets send to different node.
>> The limit is 48h. This means that after 48h (assuming that I use a
>> custom submit script with this option) all of my engines will be
>> killed and ipython will stop receiving jobs?
>
> Yes, that is right.
>
>> In other words I cannot
>> run a set of jobs that would run longer than two days using ipython?
>
> Yep, there is no way of getting around the limitations/constraints of
> the queues.
>
>> Additionally if I decide to specify max job time 48h I will most
>> likely wait longer for the appropriate nodes to become free which is
>> not really necessary when my atomic jobs run much faster.
>
> Yep, such is life on shared clusters with batch system :(
>
> What about just firing up an EC2 cluster using startcluster?
>
>> 2) I need to specify how many engines I want to use. Assuming i want
>> my set of jobs to be done as quickly as possible I should specify a
>> number that would be bigger than the number of available nodes. This
>> means that in many situations I will spawn way too many ipengines that
>> will just sit there doing nothing. This solution seems to lack
>> scalability.
>>
>> Or maybe I am using ipython/SGE in a wrong way?
>
> From what we have said, I think you are using ipython/sge in the right
> manner, you are just running into the fact that batch systems are not
> setup for truly interactive usage.
>
> Cheers,
>
> Brian
>
>> Best regards,
>> Chris
>> _______________________________________________
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>>
>
>
>
> --
> Brian E. Granger, Ph.D.
> Assistant Professor of Physics
> Cal Poly State University, San Luis Obispo
> bgranger@calpoly.edu
> ellisonbg@gmail.com
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