Hi, Am 02.05.2013 um 19:31 schrieb Happy Monk:
> Thanks for the quick reply Reuti. > > How can I restrict prolog to only certain jobs ? Here is the LSF recipe that > we are trying to implement in SGE > > > #!/bin/bash > > bsub < preproc.sh > > echo $LSB_JOBID `bsub` can change the value of an environment variable in the actual shell process - interesting. Hence it's more like a sourced script than a started child process with its own environment. > bsub -w 'done($LSB_JOBID)' < hostjob.sh > > echo $LSB_JOBID > > bsub -w 'started($LSB_JOBID)' < computejob.sh > > echo $LSB_JOBID On the hand one could add an additional environment variable to this new job, where the real condition for each "-hold_jid" is stated. But this way it would be necessary for the orignal main job to parse all outputs of all jobs for the existence of this variable. Maybe a shorter way could be to add the next job id to the context of the main job. In SGE the context of a job is meta data unrelated to SGE's handling and also unrelated to the jobs environment, it's like a comment. I mean: #!/bin/sh PREP_JOB=$(qsub -terse preproc.sh) MAIN_JOB=$(qsub -terse -hold_jid $PREP_JOB hostjob.sh) NEXT_JOB=$(qsub -terse -hold_jid $MAIN_JOB computejob.sh) qalter -ac NEXT_JOB=$NEXT_JOB $MAIN_JOB Then the prolog has to scan the `qstat -j $JOB_ID`, i.e. his own job number, whether there is an entry like: context: NEXT_JOB=1234 and if yes, use `qalter` to apply the removal only to this job id. NB: In principle there is a race condition with this setup: if the prolog of the main job runs before `qalter` for the follow up job was applied, it might miss this necessity. But this would mean that the `preproc.sh` has almost no runtime and the scheduled hostjob.sh starts more or less instantly. If this could happen it needs to be adjusted: #!/bin/sh PREP_JOB=$(qsub -terse preproc.sh) MAIN_JOB=$(qsub -terse -hold_jid $PREP_JOB -ac NEXT_JOB=PENDING hostjob.sh) NEXT_JOB=$(qsub -terse -hold_jid $MAIN_JOB computejob.sh) qalter -sc NEXT_JOB=$NEXT_JOB $MAIN_JOB Then the prolog could wait or rise an error if it sees NEXT_JOB=PENDING instead of a job id there. -- Reuti > On Thu, May 2, 2013 at 9:00 AM, Reuti <[email protected]> wrote: > Hi, > > Am 02.05.2013 um 17:10 schrieb Happy Monk: > > > Is there any way to release hold of a job immediately after the dependent > > job started, usually this hold is released after execution of the dependent > > job. > > > > This function is available in LSF but checking whether its also available > > in SGE or not. > > Not directly. You could use a queue prolog to remove the actual starting job > from all jobs which depend on this one. This makes it necessary, that all > exechosts are also submission hosts. > > To remove a complete -hold_jid list, you can give the job id 0 there to > `qalter`. As this job id will never be a real job, it always satisfies the > condition as being completed already. > > -- Reuti > _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
