Am 03.02.2014 um 13:09 schrieb Joe Borġ: > Same sleep job, ran for 12 hours without any issue in PE either. > > I can't see any CPU / MEM / IO restrictions set though, so I can't see what's > killing the proper jobs.
Is it really killed by a SIGKILL, or by something like SIGUSR1 which is by default handled in the same way in the essence (unless it's caught). (`man 7 signal`) -- Reuti > > > Regards, > Joseph David Borġ > josephb.org > > > On 31 January 2014 08:53, Joe Borġ <[email protected]> wrote: > OK, I'm now testing the same job, within a parallel environment, to see if it > has an affect. > > I can't see anywhere that I set CPU limits. > > > > Regards, > Joseph David Borġ > josephb.org > > > On 30 January 2014 11:22, Reuti <[email protected]> wrote: > Am 30.01.2014 um 11:33 schrieb Joe Borġ: > > > Did you want the output? I submitted then in a job, without a PE, on a > > different queue and it lasted the time it was meant to: > > > > $ cat test.bash.o164678 > > core file size (blocks, -c) unlimited > > data seg size (kbytes, -d) unlimited > > scheduling priority (-e) 0 > > file size (blocks, -f) unlimited > > pending signals (-i) 256644 > > max locked memory (kbytes, -l) unlimited > > max memory size (kbytes, -m) unlimited > > open files (-n) 4096 > > pipe size (512 bytes, -p) 8 > > POSIX message queues (bytes, -q) 819200 > > real-time priority (-r) 0 > > stack size (kbytes, -s) unlimited > > cpu time (seconds, -t) unlimited > > Yes, I thought about a cpu time limit by the kernel - which is not the case. > > Anyway: do you observe a difference in used CPU time and used wallclock time > as a trigger when a job is killed? As this job ran to completion, it might be > a CPU time limit somewhere. > > -- Reuti > > > > max user processes (-u) 256644 > > virtual memory (kbytes, -v) unlimited > > file locks (-x) unlimited > > core file size (blocks, -c) unlimited > > data seg size (kbytes, -d) unlimited > > scheduling priority (-e) 0 > > file size (blocks, -f) unlimited > > pending signals (-i) 256644 > > max locked memory (kbytes, -l) unlimited > > max memory size (kbytes, -m) unlimited > > open files (-n) 1024 > > pipe size (512 bytes, -p) 8 > > POSIX message queues (bytes, -q) 819200 > > real-time priority (-r) 0 > > stack size (kbytes, -s) unlimited > > cpu time (seconds, -t) unlimited > > max user processes (-u) 256644 > > virtual memory (kbytes, -v) unlimited > > file locks (-x) unlimited > > Sleeping for 12 hours zzZZZ > > Waking up > > > > > > > > > > Regards, > > Joseph David Borġ > > josephb.org > > > > > > On 27 January 2014 14:22, Reuti <[email protected]> wrote: > > Am 27.01.2014 um 11:26 schrieb Joe Borġ: > > > > > They're pretty mammoth cluster nodes. But anyway, the load is set to 99 > > > to stop it from rejecting jobs based on load (in this test queue). > > > > If you don't want load_thresholds, it can just be set to NONE. > > > > > > > We're not currently using the checkpoint feature either. > > > > Can you please submit a job with the two statements: > > > > ulimit -aH > > ulimit -aS > > > > -- Reuti > > > > > > > Regards, > > > Joseph David Borġ > > > josephb.org > > > > > > > > > On 23 January 2014 10:11, Reuti <[email protected]> wrote: > > > Hi, > > > > > > Am 23.01.2014 um 10:17 schrieb Joe Borġ: > > > > > > > First off, here is the qconf sq. Anything obvious? > > > > > > > > qname test.q > > > > hostlist @test_rack1 @test_rack2 \ > > > > @test_rack3 > > > > seq_no 0 > > > > load_thresholds load_short=99 > > > > > > What type of machine is this, with a threshold of 99? > > > > > > > suspend_thresholds NONE > > > > nsuspend 1 > > > > suspend_interval 00:05:00 > > > > priority 0 > > > > min_cpu_interval 00:05:00 > > > > processors UNDEFINED > > > > qtype BATCH INTERACTIVE > > > > ckpt_list test.ckpt > > > > > > We these jobs submitted using a checkpointing interface? > > > Is this queue subordinated to any other queue? > > > > > > --Reuti > > > > > > > > > > pe_list test.pe > > > > rerun TRUE > > > > slots 1,[@test_rack1=8],[@test_rack2=8], \ > > > > [@test_rack3=8] > > > > tmpdir /tmp > > > > shell /bin/sh > > > > prolog NONE > > > > epilog NONE > > > > shell_start_mode unix_behavior > > > > starter_method NONE > > > > suspend_method NONE > > > > resume_method NONE > > > > terminate_method NONE > > > > notify 00:00:60 > > > > owner_list NONE > > > > user_lists NONE > > > > xuser_lists NONE > > > > subordinate_list NONE > > > > complex_values NONE > > > > projects NONE > > > > xprojects NONE > > > > calendar NONE > > > > initial_state default > > > > s_rt INFINITY > > > > h_rt INFINITY > > > > s_cpu INFINITY > > > > h_cpu INFINITY > > > > s_fsize INFINITY > > > > h_fsize INFINITY > > > > s_data INFINITY > > > > h_data INFINITY > > > > s_stack INFINITY > > > > h_stack INFINITY > > > > s_core INFINITY > > > > h_core INFINITY > > > > s_rss INFINITY > > > > h_rss INFINITY > > > > s_vmem INFINITY > > > > h_vmem INFINITY > > > > > > > > > > > > > > > > > > > > Regards, > > > > Joseph David Borġ > > > > josephb.org > > > > > > > > > > > > On 17 January 2014 15:00, Reuti <[email protected]> wrote: > > > > Can you please post the output of `qconf -sq <qname>` for the queue in > > > > question and the output of `qstat -j <job_id>` for such a job. > > > > > > > > -- Reuti > > > > > > > > > > > > Am 16.01.2014 um 23:45 schrieb Joe Borġ: > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
