[IPython-User] Limitations (?) of ipython SGE support
Sun Jan 16 20:59:14 CST 2011
On Thu, Jan 13, 2011 at 7:41 AM, Chris Filo Gorgolewski
> 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
> 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
> 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.
> Best regards,
> IPython-User mailing list
Brian E. Granger, Ph.D.
Assistant Professor of Physics
Cal Poly State University, San Luis Obispo
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