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[NMusers] Usage of parallel nonmem in tendem with SGE

From: Paul Jewell [Rudraya] <pjewell_at_rudraya.com>
Date: Thu, 28 Apr 2016 16:03:45 +0000


Hello All,


I have used nonmem for a while in an environment which uses sun grid engine=
 and mpich2. Currently the two services do not interact. Batch jobs go to t=
he grid engine, and parallel jobs run across all nodes using the mpi daemon=
. This is usually not an issue, but during times of heavy user activity, th=
e amount of nonmem processes running on each compute node can exceed the to=
tal number of cores, causing inefficiency. I am looking for a method of run=
ning a parallel job such that it waits for the required number of slots / c=
ores to be available and clear of gridengine jobs before running. (and no n=
ew gridengine jobs are submitted after it until it is finished) I have seen=
 that gridengine supports parallel queues but a method of interfacing this =
with nonmem's parafile specification is not immediately apparent. I wanted =
to check if there is any possibility of using nonmem/sge in this way before=
 writing a wrapper bash script that does something like this:

-submit N number of shell scripts which sleep forever

-poll the grid engine until N number of shell scripts are seen running in t=
he queue

-begin the parallel run

-when done, qdel all of the shell scripts

This solution would some problems with evenly using cores, and would requir=
e a lot of manual code writing, so I was looking for a better solution firs=
t. Please advise if you have heard of any solution.


Thank you.

Received on Thu Apr 28 2016 - 12:03:45 EDT

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