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

Wed Feb 12 09:42:10 UTC 2020

Hey Robert,

Ask Bright support, they will help you to figure out what is going on there.

Best regards,
Taras

On Tue, Feb 11, 2020 at 8:26 PM Robert Kudyba <rkudyba at fordham.edu> wrote:

> 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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