Hi Eleonora: I think Jérémie is on the right path for your issue. If you put all of the scripts (that you normally run with qsub) in a launch script (no qsubs in this master script, just the job scripts) each job will run sequentially.
Although, as he says, maybe I'm not understanding what you are trying to do exactly. Master script would look something like: ./job1.sh ./job2.sh ... ./job34.sh Or if the scripts really are 'job#.sh': #!/bin/bash for x in $(seq 1 34); do echo "start job $x" ./job$x.sh done Launch that script with qsub, and each job should complete before the next job starts. Try it out! -Hugh On Sep 27, 2012, at 4:07 AM, "Eleonora Lusito" <[email protected]> wrote: > Hi Jérémie! > Your question is not stupid! The problem is that each run, so each qsub, is > very computationally intensive. It performs many many calculations so that I > cannot absolutely launch them all together. > > Best, > > E. > > > Jérémie Dubois-Lacoste ([email protected]) wrote: >> >> My answer may sounds so stupid that I'm sure I didn't properly get >> you problem. :-) >> Why not writing a bash script with 34 lines, one for each call to your >> 34 sh things, and then submit this "meta" script to the queuing system? >> >> Jérémie >> >> 2012/9/26 Daniel Gruber : >>> The easiest way would be to give a job a name with qsub -N job1 (or use > -terse for getting the job id) and >>> then using -hold_jid for the second job. More details you will find in > the qsub man page. Of course you >>> can also use DRMAA, or more unusual an array job with task throttling > (-tc 1). >>> >>> Daniel >>> >>> Am 26.09.2012 um 19:59 schrieb Eleonora Lusito: >>> >>>> Dear users, >>>> I have a list of .sh to run, exactly 34. I can run just a .sh job at a > time >>>> so I can launch only one qsub at a time because of the complexity of the >>>> analysis. Anyway I would like to find a way to launch a .sh script > immediately >>>> after the previous .sh script is completed. >>>> I cannot set a time to start for each job (in order to run them > consequently >>>> ) because I don't know exactly the time the script needs due to the fact > that >>>> a variable number of users are launching a variable number of script. >>>> I don't know really how this can be done. Any suggestion about? >>>> >>>> Thanks a lot >>>> >>>> >>>> E. >>>> >>>> -- >>>> Eleonora Lusito >>>> Computational Biology PhD student >>>> Molecular Medicine Program >>>> via Ripamonti 435, 20141 Milano, Italy >>>> >>>> Phone number: +390294375160 >>>> e-mail: [email protected] >>>> >>>> >>>> _______________________________________________ >>>> users mailing list >>>> [email protected] >>>> https://gridengine.org/mailman/listinfo/users >>> >>> >>> _______________________________________________ >>> users mailing list >>> [email protected] >>> https://gridengine.org/mailman/listinfo/users >> >> _______________________________________________ >> users mailing list >> [email protected] >> https://gridengine.org/mailman/listinfo/users >> > > -- > Eleonora Lusito > Computational Biology PhD student > Molecular Medicine Program > via Ripamonti 435, 20141 Milano, Italy > > Phone number: +390294375160 > e-mail: [email protected] > > > _______________________________________________ > users mailing list > [email protected] > https://gridengine.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
