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

Chris Filo Gorgolewski chris.gorgolewski@gmail....
Thu Jan 13 09:41:38 CST 2011


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:
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? In other words I cannot
run a set of jobs that would run longer than two days using ipython?
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.

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?

Best regards,
Chris


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