> Am 03.09.2015 um 03:12 schrieb Dimar Jaime González Soto > <dimar.gonzalez.s...@gmail.com>: > > It works! thank you very much. By the way, I wan to cancel or kill the > process OMA in all nodes. I tried with "qdel OMA" and only works in the > master node, the rest of the process keep running in the.slaves nodes.
This sounds that you have no tight integration of the parallel application. "control_slaves" is set to true in the PE? Does OMA use MPI or how does it perform its parallel execution? Do you submit using a PE and OMA is capable of reading the list of granted nodes? Their website is quite confusing, as they suggest to submit an array job to achieve parallelization. -- Reuti > > 2015-09-02 20:27 GMT-03:00 MacMullan, Hugh <hugh...@wharton.upenn.edu>: > Try '-b y' option (and '-j y', might as well) to your qsub command, as it's a > binary (I presume), not a job script. > > > > On Sep 2, 2015, at 4:31 PM, Dimar Jaime González Soto > <dimar.gonzalez.s...@gmail.com> wrote: > >> Hi every one, I have some issues trying to run OMA standalone >> ihttp://omabrowser.org/standalone/). I set up a grid engine network with 4 >> nodes. It seems to be running well using this script running qsub -t 1-57 >> -cwd script.sh: >> #$ -cwd >> #Merge the standard out and standard error to one file >> #$ -j y >> /bin/echo Here I am: `hostname`. Sleeping now at: `date` >> /bin/echo Running on host: `hostname`. >> /bin/echo In directory: `pwd` >> /bin/echo Starting on: `date` >> # Send mail at submission and completion of script >> #$ -m be >> #$ -M deadline@kronos >> time=60 >> if [ $# -ge 1 ]; then >> time=$1 >> fi >> sleep $time >> >> echo Now it is: `date` >> >> which generate results like: >> >> Here I am: ubuntu-node9. Sleeping now at: Wed Sep 2 17:11:44 CLT 2015 >> Running on host: ubuntu-node9. >> In directory: /home/compartido2/andres/open_reading >> Starting on: Wed Sep 2 17:11:45 CLT 2015 >> Now it is: Wed Sep 2 17:12:47 CLT 2015 >> >> the same for the rest of out files. >> >> Until here the things seem to be ok. The problem is when I try to run the >> program OMA: >> >> qsub -t 1-57 -cwd /usr/local/OMA/bin/OMA >> >> which generate 57 files OMA.e31.* and 57 files OMA.o31.*. >> >> the OMA.e* files show: >> >> Illegal variable name: >> >> and the OMA.o* files show: >> >> Warning: no access to tty (Bad file descriptor). >> Thus no job control in this shell. >> >> The process OMA without parallelization run ok. >> >> Any help would be great. >> >> cheers. >> >> -- >> Atte. >> >> Dimar González Soto >> Ingeniero Civil en Informática >> Universidad Austral de Chile >> >> >> _______________________________________________ >> users mailing list >> users@gridengine.org >> https://gridengine.org/mailman/listinfo/users > > > > -- > Atte. > > Dimar González Soto > Ingeniero Civil en Informática > Universidad Austral de Chile > > > _______________________________________________ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
