[slurm-users] after upgrade to 23.11.1 nodes stuck in completion state

Tue Jan 30 08:36:26 UTC 2024

We had similar issues with Slurm 23.11.1 (and 23.11.2). Jobs get stuck in
a completing state and slurmd daemons can't be killed because they are left
in a CLOSE-WAIT state. See my previous mail to the mailing list for the
details. And also https://bugs.schedmd.com/show_bug.cgi?id=18561 for
another site having issues.
We've now downgraded the clients (slurmd and login nodes) to 23.02.7 which
gets rid of most issues. If possible, I would try to also downgrade
slurmctld to an earlier release, but this requires getting rid of all
running and queued jobs.

Kind regards,

Fokke

Op ma 29 jan 2024 om 01:00 schreef Paul Raines <raines at nmr.mgh.harvard.edu>:

> Some more info on what I am seeing after the 23.11.3 upgrade.
>
> Here is a case where a job is cancelled but seems permanently
> stuck in 'CG' state in squeue
>
> [2024-01-28T17:34:11.002] debug3: sched: JobId=3679903 initiated
> [2024-01-28T17:34:11.002] sched: Allocate JobId=3679903 NodeList=rtx-06
> #CPUs=4 Partition=rtx8000
> [2024-01-28T17:34:11.002] debug3: create_mmap_buf: loaded file
> `/var/slurm/spool/ctld/hash.3/job.3679903/script` as buf_t
> [2024-01-28T17:42:27.724] _slurm_rpc_kill_job: REQUEST_KILL_JOB
> JobId=3679903 uid 5875902
> [2024-01-28T17:42:27.725] debug:  email msg to sg1526: Slurm
> Job_id=3679903 Name=sjob_1246 Ended, Run time 00:08:17, CANCELLED,
> ExitCode 0
> [2024-01-28T17:42:27.725] debug3: select/cons_tres: job_res_rm_job:
> JobId=3679903 action:normal
> [2024-01-28T17:42:27.725] debug3: select/cons_tres: job_res_rm_job:
> removed JobId=3679903 from part rtx8000 row 0
> [2024-01-28T17:42:27.726] job_signal: 9 of running JobId=3679903
> successful 0x8004
> [2024-01-28T17:43:19.000] Resending TERMINATE_JOB request JobId=3679903
> Nodelist=rtx-06
> [2024-01-28T17:44:20.000] Resending TERMINATE_JOB request JobId=3679903
> Nodelist=rtx-06
> [2024-01-28T17:45:20.000] Resending TERMINATE_JOB request JobId=3679903
> Nodelist=rtx-06
> [2024-01-28T17:46:20.000] Resending TERMINATE_JOB request JobId=3679903
> Nodelist=rtx-06
> [2024-01-28T17:47:20.000] Resending TERMINATE_JOB request JobId=3679903
> Nodelist=rtx-06
>
>
> So at 17:42 the user must of done an scancel.  In the slurmd log on the
> node I see:
>
> [2024-01-28T17:42:27.727] debug:  _rpc_terminate_job: uid = 1150
> JobId=3679903
> [2024-01-28T17:42:27.728] debug:  credential for job 3679903 revoked
> [2024-01-28T17:42:27.728] debug:  _rpc_terminate_job: sent SUCCESS for
> 3679903, waiting for prolog to finish
> [2024-01-28T17:42:27.728] debug:  Waiting for job 3679903's prolog to
> complete
> [2024-01-28T17:43:19.002] debug:  _rpc_terminate_job: uid = 1150
> _JobId=3679903
> [2024-01-28T17:44:20.001] debug:  _rpc_terminate_job: uid = 1150
> JobId=3679903
> [2024-01-28T17:45:20.002] debug:  _rpc_terminate_job: uid = 1150
> JobId=3679903
> [2024-01-28T17:46:20.001] debug:  _rpc_terminate_job: uid = 1150
> JobId=3679903
> [2024-01-28T17:47:20.002] debug:  _rpc_terminate_job: uid = 1150
> JobId=3679903
>
> Strange that a prolog is being called on job cancel
>
> slurmd seems to be getting the repeated calls to terminate the job
> from slurmctld but it is not happening.  Also the process table has
>
> [root at rtx-06 ~]# ps auxw | grep slurmd
> root      161784  0.0  0.0 436748 21720 ?        Ssl  13:44   0:00
> /usr/sbin/slurmd --systemd
> root      190494  0.0  0.0      0     0 ?        Zs   17:34   0:00
> [slurmd] <defunct>
>
> where there is now a zombie slurmd process I cannot kill even with kill -9
>
> If I do a 'systemctl stop slurmd' it takes a long time but eventually stop
> slurmd and gets rid of the zombie process but kills the "good" running
> jobs too with NODE_FAIL.
>
> Another case is where a job will be cancelled and SLURM acts like it
> is cancelled with it not showing up in squeue but the process keep running
> on the box.
>
> # pstree -u sg1526 -p | grep ^slurm
> slurm_script(185763)---python(185796)-+-{python}(185797)
> # strings /proc/185763/environ | grep JOB_ID
> SLURM_JOB_ID=3679888
> # squeue -j 3679888
> slurm_load_jobs error: Invalid job id specified
>
> sacct shows that job being cancelled.  In the slurmd log we see
>
> [2024-01-28T17:33:58.757] debug:  _rpc_terminate_job: uid = 1150
> JobId=3679888
> [2024-01-28T17:33:58.757] debug:  credential for job 3679888 revoked
> [2024-01-28T17:33:58.757] debug:  _step_connect: connect() failed for
> /var/slurm/spool/d/rtx-06_3679888.4294967292: Connection refused
> [2024-01-28T17:33:58.757] debug:  Cleaned up stray socket
> /var/slurm/spool/d/rtx-06_3679888.4294967292
> [2024-01-28T17:33:58.757] debug:  signal for nonexistent
> StepId=3679888.extern stepd_connect failed: Connection refused
> [2024-01-28T17:33:58.757] debug:  _step_connect: connect() failed for
> /var/slurm/spool/d/rtx-06_3679888.4294967291: Connection refused
> [2024-01-28T17:33:58.757] debug:  Cleaned up stray socket
> /var/slurm/spool/d/rtx-06_3679888.4294967291
> [2024-01-28T17:33:58.757] _handle_stray_script: Purging vestigial job
> script /var/slurm/spool/d/job3679888/slurm_script
> [2024-01-28T17:33:58.757] debug:  signal for nonexistent
> StepId=3679888.batch stepd_connect failed: Connection refused
> [2024-01-28T17:33:58.757] debug2: No steps in jobid 3679888 were able to
> be signaled with 18
> [2024-01-28T17:33:58.757] debug2: No steps in jobid 3679888 to send signal
> 15
> [2024-01-28T17:33:58.757] debug2: set revoke expiration for jobid 3679888
> to 1706481358 UTS
> [2024-01-28T17:33:58.757] debug:  Waiting for job 3679888's prolog to
> complete
> [2024-01-28T17:33:58.757] debug:  Finished wait for job 3679888's prolog
> to complete
> [2024-01-28T17:33:58.771] debug:  completed epilog for jobid 3679888
> [2024-01-28T17:33:58.774] debug:  JobId=3679888: sent epilog complete msg:
> rc = 0
>
>
> -- Paul Raines (http://help.nmr.mgh.harvard.edu)
>
>
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-- 
Fokke Dijkstra <f.dijkstra at rug.nl> <f.dijkstra at rug.nl>
Team High Performance Computing
Center for Information Technology, University of Groningen
Postbus 11044, 9700 CA  Groningen, The Netherlands
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