Hi, Am 26.10.2012 um 19:37 schrieb Metzler, Chris:
> #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; Yes, as it might oversubscribe your granted slot count, or some scripts try to jump out of the process tree and might get out of SGE's control (these could be caught the additional group id though). But there are exceptions of course. a) define a PE with "allocation_rule $pe_slots" b) request the overall slot count during the submission with the PE: qsub -pe smp 3 foobar.sh # in case you have just 3 serial tasks qsub -pe smp 5 foobar.sh # for your example below c) Put a` wait` at the end of the script, so that it wait for the completion of all started background processes NB: yes, it's good to set OMP_NUM_THREADS by hand, as sometimes the number of cores found in the executing machine us used as default, hence all threads would use all cores - which is seldom practical. -- Reuti > 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 > > _______________________________________________ > users mailing list > [email protected] > https://gridengine.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
