[slurm-users] Node appears to have a different slurm.conf than the slurmctld; update_node: node reason set to: Kill task failed

Tue Feb 11 17:26:11 UTC 2020

This is still happening. Nodes are being drained after a kill task failed.
Could this be related to https://bugs.schedmd.com/show_bug.cgi?id=6307?

[2020-02-11T12:21:26.005] update_node: node node001 reason set to: Kill
task failed
[2020-02-11T12:21:26.006] update_node: node node001 state set to DRAINING
[2020-02-11T12:21:26.006] got (nil)
[2020-02-11T12:21:26.015] error: slurmd error running JobId=1514 on
node(s)=node001: Kill task failed
[2020-02-11T12:21:26.015] _job_complete: JobID=1514 State=0x1 NodeCnt=1
WEXITSTATUS 1
[2020-02-11T12:21:26.015] email msg to sli339 at fordham.edu: SLURM
Job_id=1514 Name=run.sh Failed, Run time 00:02:21, NODE_FAIL, ExitCode 0
[2020-02-11T12:21:26.016] _job_complete: requeue JobID=1514 State=0x8000
NodeCnt=1 per user/system request
[2020-02-11T12:21:26.016] _job_complete: JobID=1514 State=0x8000 NodeCnt=1
done
[2020-02-11T12:21:26.057] Requeuing JobID=1514 State=0x0 NodeCnt=0
[2020-02-11T12:21:46.985] _job_complete: JobID=1511 State=0x1 NodeCnt=1
WEXITSTATUS 0
[2020-02-11T12:21:46.985] _job_complete: JobID=1511 State=0x8003 NodeCnt=1
done
[2020-02-11T12:21:52.111] _job_complete: JobID=1512 State=0x1 NodeCnt=1
WEXITSTATUS 0
[2020-02-11T12:21:52.112] _job_complete: JobID=1512 State=0x8003 NodeCnt=1
done
[2020-02-11T12:21:52.214] sched: Allocate JobID=1516 NodeList=node002
#CPUs=1 Partition=defq
[2020-02-11T12:21:52.483] _job_complete: JobID=1513 State=0x1 NodeCnt=1
WEXITSTATUS 0
[2020-02-11T12:21:52.483] _job_complete: JobID=1513 State=0x8003 NodeCnt=1
done

On Tue, Feb 11, 2020 at 11:54 AM Robert Kudyba <rkudyba at fordham.edu> wrote:

> Usually means you updated the slurm.conf but have not done "scontrol
>> reconfigure" yet.
>>
> Well it turns out it was something else related to a Bright Computing
> setting. In case anyone finds this thread in the future:
>
> ourcluster->category[gpucategory]->roles]% use slurmclient
> [ourcluster->category[gpucategory]->roles[slurmclient]]% show
> ...
> RealMemory 196489092
> ...
> [ ciscluster->category[gpucategory]->roles[slurmclient]]%
>
> Values are specified in MB and this line is saying that our node has 196TB
> of RAM.
>
> I set this using cmsh:
>
> # cmsh
> % category
> % use gpucategory
> % roles
> % use slurmclient
> % set realmemory 191846
> % commit
>
> The value in /etc/slurm/slurm.conf was conflicting with this especially
> when restarting slurmctld.
>
> On 2/10/2020 8:55 AM, Robert Kudyba wrote:
>>
>> We are using Bright Cluster 8.1 with and just upgraded to slurm-17.11.12.
>>
>> We're getting the below errors when I restart the slurmctld service. The
>> file appears to be the same on the head node and compute nodes:
>> [root at node001 ~]# ls -l /cm/shared/apps/slurm/var/etc/slurm.conf
>>
>> -rw-r--r-- 1 root root 3477 Feb 10 11:05
>> /cm/shared/apps/slurm/var/etc/slurm.conf
>>
>> [root at ourcluster ~]# ls -l  /cm/shared/apps/slurm/var/etc/slurm.conf
>> /etc/slurm/slurm.conf
>>
>> -rw-r--r-- 1 root root 3477 Feb 10 11:05
>> /cm/shared/apps/slurm/var/etc/slurm.conf
>>
>> lrwxrwxrwx 1 root root   40 Nov 30  2018 /etc/slurm/slurm.conf ->
>> /cm/shared/apps/slurm/var/etc/slurm.conf
>>
>> So what else could be causing this?
>> [2020-02-10T10:31:08.987] mcs: MCSParameters = (null). ondemand set.
>> [2020-02-10T10:31:12.009] error: Node node001 appears to have a different
>> slurm.conf than the slurmctld.  This could cause issues with communication
>> and functionality.  Please review both files and make  sure they are the
>> same.  If this is expected ignore, and set DebugFlags=NO_CONF_HASH in your
>> slurm.conf.
>> [2020-02-10T10:31:12.009] error: Node node001 has low real_memory size
>> (191846 < 196489092)
>> [2020-02-10T10:31:12.009] error: _slurm_rpc_node_registration
>> node=node001: Invalid argument
>> [2020-02-10T10:31:12.011] error: Node node002 appears to have a different
>> slurm.conf than the slurmctld.  This could cause issues with communication
>> and functionality.  Please review both files and make sure they are the
>> same.  If this is expected ignore, and set DebugFlags=NO_CONF_HASH in your
>> slurm.conf.
>> [2020-02-10T10:31:12.011] error: Node node002 has low real_memory size
>> (191840 < 196489092)
>> [2020-02-10T10:31:12.011] error: _slurm_rpc_node_registration
>> node=node002: Invalid argument
>> [2020-02-10T10:31:12.047] error: Node node003 appears to have a different
>> slurm.conf than the slurmctld.  This could cause issues with communication
>> and functionality.  Please review both files and make sure they are the
>> same.  If this is expected ignore, and set DebugFlags=NO_CONF_HASH in your
>> slurm.conf.
>> [2020-02-10T10:31:12.047] error: Node node003 has low real_memory size
>> (191840 < 196489092)
>> [2020-02-10T10:31:12.047] error: Setting node node003 state to DRAIN
>> [2020-02-10T10:31:12.047] drain_nodes: node node003 state set to DRAIN
>> [2020-02-10T10:31:12.047] error: _slurm_rpc_node_registration
>> node=node003: Invalid argument
>> [2020-02-10T10:32:08.026]
>> SchedulerParameters=default_queue_depth=100,max_rpc_cnt=0,max_sched_time=2,partition_job_depth=0,sched_max_job_start=0,sched_min_interval=2
>> [2020-02-10T10:56:08.988] Processing RPC: REQUEST_RECONFIGURE from uid=0
>> [2020-02-10T10:56:08.992] layouts: no layout to initialize
>> [2020-02-10T10:56:08.992] restoring original state of nodes
>> [2020-02-10T10:56:08.992] cons_res: select_p_node_init
>> [2020-02-10T10:56:08.992] cons_res: preparing for 2 partitions
>> [2020-02-10T10:56:08.992] _preserve_plugins: backup_controller not
>> specified
>> [2020-02-10T10:56:08.992] cons_res: select_p_reconfigure
>> [2020-02-10T10:56:08.992] cons_res: select_p_node_init
>> [2020-02-10T10:56:08.992] cons_res: preparing for 2 partitions
>> [2020-02-10T10:56:08.992] No parameter for mcs plugin, default values set
>> [2020-02-10T10:56:08.992] mcs: MCSParameters = (null). ondemand set.
>> [2020-02-10T10:56:08.992] _slurm_rpc_reconfigure_controller: completed
>> usec=4369
>> [2020-02-10T10:56:11.253]
>> SchedulerParameters=default_queue_depth=100,max_rpc_cnt=0,max_sched_time=2,partition_job_depth=0,sched_max_job_start=0,sched_min_interval=2
>> [2020-02-10T10:56:18.645] update_node: node node001 reason set to: hung
>> [2020-02-10T10:56:18.645] update_node: node node001 state set to DOWN
>> [2020-02-10T10:56:18.645] got (nil)
>> [2020-02-10T10:56:18.679] update_node: node node001 state set to IDLE
>> [2020-02-10T10:56:18.679] got (nil)
>> [2020-02-10T10:56:18.693] update_node: node node002 reason set to: hung
>> [2020-02-10T10:56:18.693] update_node: node node002 state set to DOWN
>> [2020-02-10T10:56:18.693] got (nil)
>> [2020-02-10T10:56:18.711] update_node: node node002 state set to IDLE
>> [2020-02-10T10:56:18.711] got (nil)
>>
>> And not sure if this is related but we're getting this  "Kill task
>> failed" and a node gets drained.
>>
>> [2020-02-09T14:42:06.006] error: slurmd error running JobId=1465 on
>> node(s)=node001: Kill task failed
>> [2020-02-09T14:42:06.006] _job_complete: JobID=1465 State=0x1 NodeCnt=1
>> WEXITSTATUS 1
>> [2020-02-09T14:42:06.006] email msg to ouruser at ourdomain.edu: SLURM
>> Job_id=1465 Name=run.sh Failed, Run time 00:02:23, NODE_FAIL, ExitCode 0
>> [2020-02-09T14:42:06.006] _job_complete: requeue JobID=1465 State=0x8000
>> NodeCnt=1 per user/system request
>> [2020-02-09T14:42:06.006] _job_complete: JobID=1465 State=0x8000
>> NodeCnt=1 done
>> [2020-02-09T14:42:06.017] Requeuing JobID=1465 State=0x0 NodeCnt=0
>> [2020-02-09T14:43:16.308] backfill: Started JobID=1466 in defq on node003
>> [2020-02-09T14:43:17.054] prolog_running_decr: Configuration for
>> JobID=1466 is complete
>> [2020-02-09T14:44:16.309] email msg to ouruser at ourdomain.edu:: SLURM
>> Job_id=1461 Name=run.sh Began, Queued time 00:02:14
>> [2020-02-09T14:44:16.309] backfill: Started JobID=1461 in defq on node003
>> [2020-02-09T14:44:16.309] email msg to ouruser at ourdomain.edu:: SLURM
>> Job_id=1465 Name=run.sh Began, Queued time 00:02:10
>> [2020-02-09T14:44:16.309] backfill: Started JobID=1465 in defq on node003
>> [2020-02-09T14:44:16.850] prolog_running_decr: Configuration for
>> JobID=1461 is complete
>> [2020-02-09T14:44:17.040] prolog_running_decr: Configuration for
>> JobID=1465 is complete
>> [2020-02-09T14:44:27.016] error: slurmd error running JobId=1466 on
>> node(s)=node003: Kill task failed
>> [2020-02-09T14:44:27.016] drain_nodes: node node003 state set to DRAIN
>> [2020-02-09T14:44:27.016] _job_complete: JobID=1466 State=0x1 NodeCnt=1
>> WEXITSTATUS 1
>> [2020-02-09T14:44:27.016] _job_complete: requeue JobID=1466 State=0x8000
>> NodeCnt=1 per user/system request
>> [2020-02-09T14:44:27.017] _job_complete: JobID=1466 State=0x8000
>> NodeCnt=1 done
>> [2020-02-09T14:44:27.057] Requeuing JobID=1466 State=0x0 NodeCnt=0
>> [2020-02-09T14:44:27.081] update_node: node node003 reason set to: Kill
>> task failed
>> [2020-02-09T14:44:27.082] update_node: node node003 state set to DRAINING
>> [2020-02-09T14:44:27.082] got (nil)
>> [2020-02-09T14:45:33.098] _job_complete: JobID=1461 State=0x1 NodeCnt=1
>> WEXITSTATUS 1
>> [2020-02-09T14:45:33.098] email msg to ouruser at ourdomain.edu:: SLURM
>> Job_id=1461 Name=run.sh Failed, Run time 00:01:17, FAILED, ExitCode 1
>>
>> Could this be related to https://bugs.schedmd.com/show_bug.cgi?id=6307
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bugs.schedmd.com_show-5Fbug.cgi-3Fid-3D6307&d=DwMDaQ&c=aqMfXOEvEJQh2iQMCb7Wy8l0sPnURkcqADc2guUW8IM&r=X0jL9y0sL4r4iU_qVtR3lLNo4tOL1ry_m7-psV3GejY&m=m9sYnr-lCssLr6zMcdaFYgSoAl0x7ah_IDtueXpIpZI&s=po2vRnNiVM3rBAFDtfkqGJuglAnL9reBDbDvmtWWBk8&e=>
>> ?
>>
>>
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