Only in qsub
Regards, Joseph David Borġ josephb.org On 16 January 2014 16:59, Reuti <[email protected]> wrote: > Am 16.01.2014 um 17:17 schrieb Joe Borġ: > > > I checked with qstat -j and the value displayed (in seconds) were > correct. > > > > With qacct, I get > > > > failed 100 : assumedly after job > > exit_status 137 > > > > Seeing as they were all killed at the exact same run time, I can't see > what else could have done it. > > As mentioned, was there something in the messages file like: > > 01/16/2014 17:54:46| main|pc15370|W|job 10561.1 exceeded hard wallclock > time - initiate terminate method > > Is the limit in the `qsub` command or in the queue definition? > > -- Reuti > > > > Regards, > > Joseph David Borġ > > josephb.org > > > > > > On 15 January 2014 20:30, Reuti <[email protected]> wrote: > > Hi, > > > > Am 15.01.2014 um 18:55 schrieb Joe Borġ: > > > > > I have it working, except even if I put jobs run time as 24 hours, > they all get killed after 6hours 40mins. > > > > 6h 40m = 360m + 40m = 400m = 24000s - did you forget by accident the > colons when you defined the limit? > > > > > > > Looking at qstat -j shows the correct number of seconds against > hard_resource_list h_rt. > > > > > > Any ideas? > > > > Was it really killed by SGE: is there any hint in the messages file of > the node, i.e. something like /var/spool/sge/node01/messages about the > reason for the kill ("loglevel log_info" in the `qconf -mconf`)?. > > > > -- Reuti > > > > > > > Regards, > > > Joseph David Borġ > > > josephb.org > > > > > > > > > On 15 January 2014 10:24, Reuti <[email protected]> wrote: > > > Hi, > > > > > > Am 15.01.2014 um 11:16 schrieb Joe Borġ: > > > > > > > Using h_rt kills the job after the allotted time. > > > > > > Yes. > > > > > > > > > > Can't this be disabled? > > > > > > There is no feature in SGE to extend the granted runtime of a job (I > heard such a thing is available in Torque). > > > > > > > > > > We only want to use it as a rough guide. > > > > > > If you want to do it only once in a time for a particular job: > > > > > > In this case you can just kill (or softstop) the `sgeexecd` on the > node. You will lose control of the jobs on the node and the node (from > SGE's view - `qhost` shows "-" for the node's load). So you have to check > from time to time whether the job in question finished already, and then > restart the `sgeexecd`. Also no new jobs will be scheduled to the node. > > > > > > Only at point of restarting the `sgeexecd` it will discover that the > job finished (and send an email if applicable). Other (still) running jobs > will gain supervision of their runtime again. > > > > > > -- Reuti > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > Regards, > > > > Joseph David Borġ > > > > josephb.org > > > > > > > > > > > > On 13 January 2014 17:43, Reuti <[email protected]> wrote: > > > > Am 13.01.2014 um 18:33 schrieb Joe Borġ: > > > > > > > > > Thanks. Can you please tell me what I'm doing wrong? > > > > > > > > > > qsub -q test.q -R y -l h_rt=60 -pe test.pe 1 small.bash > > > > > qsub -q test.q -R y -l h_rt=120 -pe test.pe 2 big.bash > > > > > qsub -q test.q -R y -l h_rt=60 -pe test.pe 1 small.bash > > > > > qsub -q test.q -R y -l h_rt=60 -pe test.pe 1 small.bash > > > > > > > > Only the parallel job needs "-R y". > > > > > > > > > > > > > > > > > > job-ID prior name user state submit/start at > queue slots ja-task-ID > > > > > > ----------------------------------------------------------------------------------------------------------------- > > > > > 156757 0.50000 small.bash joe.borg qw 01/13/2014 16:45:18 > 1 > > > > > 156761 0.50000 big.bash joe.borg qw 01/13/2014 16:55:31 > 2 > > > > > 156762 0.50000 small.bash joe.borg qw 01/13/2014 16:55:33 > 1 > > > > > 156763 0.50000 small.bash joe.borg qw 01/13/2014 16:55:34 > 1 > > > > > > > > > > ...But when I release... > > > > > > > > max_reservation is set? > > > > > > > > But the reservation feature must also be seen in a running cluster. > If all four jobs are on hold and released at once, I wouldn't be surprised > if it's not strictly FIFO. > > > > > > > > > > > > > job-ID prior name user state submit/start at > queue slots ja-task-ID > > > > > > ----------------------------------------------------------------------------------------------------------------- > > > > > 156757 0.50000 small.bash joe.borg r 01/13/2014 16:56:06 > test.q@test 1 > > > > > 156762 0.50000 small.bash joe.borg r 01/13/2014 16:56:06 > test.q@test 1 > > > > > 156761 0.50000 big.bash joe.borg qw 01/13/2014 16:55:31 > 2 > > > > > 156763 0.50000 small.bash joe.borg qw 01/13/2014 16:55:34 > 1 > > > > > > > > As job 156762 has the same runtime as 156757, backfilling will occur > to use the otherwise idling core. Whether job 156762 is started or not, the > parallel one 156761 will start at the same time. Only 156763 shouldn't > start. > > > > > > > > -- Reuti > > > > > > > > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > > > Regards, > > > > > Joseph David Borġ > > > > > josephb.org > > > > > > > > > > > > > > > On 13 January 2014 17:26, Reuti <[email protected]> > wrote: > > > > > Am 13.01.2014 um 17:24 schrieb Joe Borġ: > > > > > > > > > > > Hi Reuti, > > > > > > > > > > > > I am using a PE, so that's fine. > > > > > > > > > > > > I've not set either of the other 3. Will the job be killed if > default_duration is exceeded? > > > > > > > > > > No. It can be set to any value you like (like a few weeks), but it > shouldn't be set to "INFINITY" as SGE judges infinity being smaller than > infinity and so backfilling will always occur. > > > > > > > > > > -- Reuti > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > Joseph David Borġ > > > > > > josephb.org > > > > > > > > > > > > > > > > > > On 13 January 2014 16:16, Reuti <[email protected]> > wrote: > > > > > > Hi, > > > > > > > > > > > > Am 13.01.2014 um 16:58 schrieb Joe Borġ: > > > > > > > > > > > > > I'm trying to set up an SGE queue and am having a problem > getting the jobs to start in the right order. Here is my example - test.q > with 2 possible slots and the following jobs queued: > > > > > > > > > > > > > > job-ID prior name user state submit/start at > queue slots ja-task-ID > > > > > > > > ----------------------------------------------------------------------------------------------------------------- > > > > > > > 1 0.50000 small.bash joe.borg qw 01/13/2014 > 15:43:16 1 > > > > > > > 2 0.50000 big.bash joe.borg qw 01/13/2014 > 15:43:24 2 > > > > > > > 3 0.50000 small.bash joe.borg qw 01/13/2014 > 15:43:27 1 > > > > > > > 4 0.50000 small.bash joe.borg qw 01/13/2014 > 15:43:28 1 > > > > > > > > > > > > > > I want the jobs to run in that order, but (obviously), when I > enable the queue, the small jobs fill the available slots and the big job > has to wait for them to complete. I'd like it setup so that only job 1 > runs; finishes, then 2 (with both slots), then the final 2 jobs, 3 & 4, > together. > > > > > > > > > > > > > > I've looked at -R y on submission, but doesn't seem to work. > > > > > > > > > > > > For the reservation to work (and it's only necessary to request > it for the parallel job) it's necessary to have suitable "h_rt" requests > for all jobs. > > > > > > > > > > > > - Do you request any "h_rt" for all jobs? > > > > > > - Do you have a "default_duration" set to a proper value in the > schedule configuration otherwise? > > > > > > - Is "max_reservation" set to a value like 16? > > > > > > > > > > > > -- Reuti > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > Joseph David Borġ > > > > > > > josephb.org > > > > > > > _______________________________________________ > > > > > > > users mailing list > > > > > > > [email protected] > > > > > > > https://gridengine.org/mailman/listinfo/users > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
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