Angelos,
I'm glad you mentioned UnkillableStepProgram. We meant to look at that
a while ago but forgot about it. That will be very useful for us as
well, though the answer for us is pretty much always Lustre problems.
Ryan
On 7/22/20 1:02 PM, Angelos Ching wrote:
Agreed. You may also want to write a script that gather the list of
program in "D state" (kernel wait) and print their stack; and
configure it as UnkillableStepProgram so that you can capture the
program and relevant system callS that caused the job to become
unkillable / timed out exiting for further troubleshooting.
Regards,
Angelos
(Sent from mobile, please pardon me for typos and cursoriness.)
2020/07/23 0:41、Ryan Cox <ryan_...@byu.edu>のメール:
Ivan,
Are you having I/O slowness? That is the most common cause for us. If
it's not that, you'll want to look through all the reasons that it
takes a long time for a process to actually die after a SIGKILL
because one of those is the likely cause. Typically it's because the
process is waiting for an I/O syscall to return. Sometimes swap death
is the culprit, but usually not at the scale that you stated. Maybe
you could try reproducing the issue manually or putting something in
epilog the see the state of the processes in the job's cgroup.
Ryan
On 7/22/20 10:24 AM, Ivan Kovanda wrote:
Dear slurm community,
Currently running slurm version 18.08.4
We have been experiencing an issue causing any nodes a slurm job was
submitted to to "drain".
From what I've seen, it appears that there is a problem with how
slurm is cleaning up the job with the SIGKILL process.
I've found this slurm article
(https://slurm.schedmd.com/troubleshoot.html#completing) , which has
a section titled "Jobs and nodes are stuck in COMPLETING state",
where it recommends increasing the "UnkillableStepTimeout" in the
slurm.conf , but all that has done is prolong the time it takes for
the job to timeout.
The default time for the "UnkillableStepTimeout" is 60 seconds.
After the job completes, it stays in the CG (completing) status for
the 60 seconds, then the nodes the job was submitted to go to drain
status.
On the headnode running slurmctld, I am seeing this in the log -
/var/log/slurmctld:
--------------------------------------------------------------------------------------------------------------------------------------------
[2020-07-21T22:40:03.000] update_node: node node001 reason set to:
Kill task failed
[2020-07-21T22:40:03.001] update_node: node node001 state set to
DRAINING
On the compute node, I am seeing this in the log - /var/log/slurmd
--------------------------------------------------------------------------------------------------------------------------------------------
[2020-07-21T22:38:33.110] [1485.batch] done with job
[2020-07-21T22:38:33.110] [1485.extern] Sent signal 18 to
1485.4294967295
[2020-07-21T22:38:33.111] [1485.extern] Sent signal 15 to
1485.4294967295
[2020-07-21T22:39:02.820] [1485.extern] Sent SIGKILL signal to
1485.4294967295
[2020-07-21T22:40:03.000] [1485.extern] error: *** EXTERN STEP FOR
1485 STEPD TERMINATED ON node001 AT 2020-07-21T22:40:02 DUE TO JOB
NOT ENDING WITH SIGNALS ***
I've tried restarting the SLURMD daemon on the compute nodes, and
even completing rebooting a few computes nodes (node001, node002) .
From what I've seen were experiencing this on all nodes in the cluster.
I've yet to restart the headnode because there are still active jobs
on the system so I don't want to interrupt those.
Thank you for your time,
Ivan
