[gridengine users] Q: how to set up a job in which multiple executables run simultaneously? Also: Open MP environment variables honored?

Metzler, Chris christopher.metzler at nrl.navy.mil
Fri Oct 26 17:37:06 UTC 2012


Hi.  I'm new to submitting jobs through Grid Engine, and have skimmed users guides, googled, etc., without figuring this out and could use some advice.

#1:  I need to be able to submit jobs that will start up several distinct executables that need to run at the same time. If I was doing my work in an interactive shell, I'd just do something like this:

$ foo &
$ bar &
$ baz &

. . .and so they'd all start around the same time, run in the background, and complete around the same time. The executables talk to each other through the output files, and I don't need to do any more than that.

But from what I've read in users guides, I shouldn't invoke processes in the background in jobs submitted to GE; and that makes sense to me, since then the interpreter would reach the bottom of the script while the executables are still running. But submitting a script with contents of:

foo
bar
baz

won't work, because those are run sequentially.

The only thing I can think of to do is to separate each executable out into its own job submitted to the queue; but then I need to guarantee that they start executing at the same time, rather than two starting while one sits in a pending state.

#2:  Normally, when running these interactively, I'd set them up for Open MP use doing something like this:

$ setenv OMP_NUM_THREADS 1
$ foo &
$ setenv OMP_NUM_THREADS 2
$ bar &
$ baz &
etc.

Will instructions like that be honored within a script submitted to the scheduler?

Any advice on these would be very helpful. Thanks much.

-c

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