[slurm-users] Slurmd enabled crash with CgroupV2
Tristan LEFEBVRE
Hello to all,
I'm trying to do an installation of Slurm with cgroupv2 activated.
But I'm facing an odd thing : when slurmd is enabled it crash at the next reboot and will never start unless i disable it.
Here is a full example of the situation
[root@compute ~]# systemctl start slurmd
[root@compute ~]# systemctl status slurmd
● slurmd.service - Slurm node daemon
Loaded: loaded (/usr/lib/systemd/system/slurmd.service; disabled; vendor preset: disabled)
Active: active (running) since Fri 2023-03-10 15:57:00 CET; 967ms ago
Main PID: 8053 (slurmd)
Tasks: 1
Memory: 3.1M
CGroup: /system.slice/slurmd.service
└─8053 /opt/slurm_bin/sbin/slurmd -D --conf-server XXXXX:6817 -s
mars 10 15:57:00 compute.cluster.lab systemd[1]: Started Slurm node daemon.
mars 10 15:57:00 compute.cluster.lab slurmd[8053]: slurmd: slurmd version 23.02.0 started
mars 10 15:57:00 compute.cluster.lab slurmd[8053]: slurmd: slurmd started on Fri, 10 Mar 2023 15:57:00 +0100
mars 10 15:57:00 compute.cluster.lab slurmd[8053]: slurmd: CPUs=48 Boards=1 Sockets=2 Cores=24 Threads=1 Memory=385311 TmpDisk=19990 Uptime=12>
[root@compute ~]# systemctl enable slurmd
Created symlink /etc/systemd/system/multi-user.target.wants/slurmd.service → /usr/lib/systemd/system/slurmd.service.
[root@compute ~]# reboot now
> [ reboot of the node]
[adm@compute ~]$ sudo systemctl status slurmd
● slurmd.service - Slurm node daemon
Loaded: loaded (/usr/lib/systemd/system/slurmd.service; enabled; vendor preset: disabled)
Active: failed (Result: exit-code) since Fri 2023-03-10 16:00:33 CET; 1min 0s ago
Process: 2659 ExecStart=/opt/slurm_bin/sbin/slurmd -D --conf-server XXXX:6817 -s $SLURMD_OPTIONS (code=exited, status=1/FAILURE)
Main PID: 2659 (code=exited, status=1/FAILURE)
mars 10 16:00:33 compute.cluster.lab slurmd[2659]: slurmd: slurmd version 23.02.0 started
mars 10 16:00:33 compute.cluster.lab slurmd[2659]: slurmd: error: Controller cpuset is not enabled!
mars 10 16:00:33 compute.cluster.lab slurmd[2659]: slurmd: error: Controller cpu is not enabled!
mars 10 16:00:33 compute.cluster.lab slurmd[2659]: slurmd: error: cpu cgroup controller is not available.
mars 10 16:00:33 compute.cluster.lab slurmd[2659]: slurmd: error: There's an issue initializing memory or cpu controller
mars 10 16:00:33 compute.cluster.lab slurmd[2659]: slurmd: error: Couldn't load specified plugin name for jobacct_gather/cgroup: Plugin init()>
mars 10 16:00:33 compute.cluster.lab slurmd[2659]: slurmd: error: cannot create jobacct_gather context for jobacct_gather/cgroup
mars 10 16:00:33 compute.cluster.lab slurmd[2659]: slurmd: fatal: Unable to initialize jobacct_gather
mars 10 16:00:33 compute.cluster.lab systemd[1]: slurmd.service: Main process exited, code=exited, status=1/FAILURE
mars 10 16:00:33 compute.cluster.lab systemd[1]: slurmd.service: Failed with result 'exit-code'.
[adm@compute ~]$ sudo systemctl start slurmd
[adm@compute ~]$ sudo systemctl status slurmd
● slurmd.service - Slurm node daemon
Loaded: loaded (/usr/lib/systemd/system/slurmd.service; enabled; vendor preset: disabled)
Active: failed (Result: exit-code) since Fri 2023-03-10 16:01:37 CET; 1s ago
Process: 3321 ExecStart=/opt/slurm_bin/sbin/slurmd -D --conf-server XXXX:6817 -s $SLURMD_OPTIONS (code=exited, status=1/FAILURE)
Main PID: 3321 (code=exited, status=1/FAILURE)
mars 10 16:01:37 compute.cluster.lab slurmd[3321]: slurmd: slurmd version 23.02.0 started
mars 10 16:01:37 compute.cluster.lab slurmd[3321]: slurmd: error: Controller cpuset is not enabled!
mars 10 16:01:37 compute.cluster.lab slurmd[3321]: slurmd: error: Controller cpu is not enabled!
mars 10 16:01:37 compute.cluster.lab slurmd[3321]: slurmd: error: cpu cgroup controller is not available.
mars 10 16:01:37 compute.cluster.lab slurmd[3321]: slurmd: error: There's an issue initializing memory or cpu controller
mars 10 16:01:37 compute.cluster.lab slurmd[3321]: slurmd: error: Couldn't load specified plugin name for jobacct_gather/cgroup: Plugin init()>
mars 10 16:01:37 compute.cluster.lab slurmd[3321]: slurmd: error: cannot create jobacct_gather context for jobacct_gather/cgroup
mars 10 16:01:37 compute.cluster.lab slurmd[3321]: slurmd: fatal: Unable to initialize jobacct_gather
mars 10 16:01:37 compute.cluster.lab systemd[1]: slurmd.service: Main process exited, code=exited, status=1/FAILURE
mars 10 16:01:37 compute.cluster.lab systemd[1]: slurmd.service: Failed with result 'exit-code'.
[adm@compute ~]$ sudo systemctl disable slurmd
Removed /etc/systemd/system/multi-user.target.wants/slurmd.service.
[adm@compute ~]$ sudo systemctl start slurmd
[adm@compute ~]$ sudo systemctl status slurmd
● slurmd.service - Slurm node daemon
Loaded: loaded (/usr/lib/systemd/system/slurmd.service; disabled; vendor preset: disabled)
Active: active (running) since Fri 2023-03-10 16:01:45 CET; 1s ago
Main PID: 3358 (slurmd)
Tasks: 1
Memory: 6.1M
CGroup: /system.slice/slurmd.service
└─3358 /opt/slurm_bin/sbin/slurmd -D --conf-server XXXX:6817 -s
mars 10 16:01:45 compute.cluster.lab systemd[1]: Started Slurm node daemon.
mars 10 16:01:45 compute.cluster.lab slurmd[3358]: slurmd: slurmd version 23.02.0 started
mars 10 16:01:45 compute.cluster.lab slurmd[3358]: slurmd: slurmd started on Fri, 10 Mar 2023 16:01:45 +0100
mars 10 16:01:45 compute.cluster.lab slurmd[3358]: slurmd: CPUs=48 Boards=1 Sockets=2 Cores=24 Threads=1 Memory=385311 TmpDisk=19990 Uptime=84>
As you can see. Slurmd successfully start only when not enable after a reboot.- I'm using Rocky Linux 8 and I've configured cgroupv2 with grubby
> grubby --update-kernel=ALL --args="systemd.unified_cgroup_hierarchy=1 systemd.legacy_systemd_cgroup_controller=0 cgroup_no_v1=all"
- Slurm 23.02 is build with rpmbuild and slurmd on the compute node is installed with rpm
- Here is my cgroup.conf :
CgroupPlugin=cgroup/v2 ConstrainCores=yes ConstrainRAMSpace=yes ConstrainSwapSpace=yes ConstrainDevices=no
And my slurm.conf have :
ProctrackType=proctrack/cgroup TaskPlugin=task/cgroup,task/affinity JobAcctGatherType=jobacct_gather/cgroup
- If i do "systemctl start slurmd" on a compute node it's a success.
- If i do "systemctl enable slurmd" and then "systemctl restart slurmd" it's still ok
- if i enable and reboot, slurmd send this error :
slurmd: error: Controller cpuset is not enabled! slurmd: error: Controller cpu is not enabled! slurmd: error: cpu cgroup controller is not available. slurmd: error: There's an issue initializing memory or cpu controlle
- I've done some research and read about cgroup.subtree_control. And so if i do:
cat /sys/fs/cgroup/cgroup.subtree_control memory pids
So I've tried to follow the RedHat documentation with there example : ( the link of the RedHat page
here )
echo "+cpu" >> /sys/fs/cgroup/cgroup.subtree_control
echo "+cpuset" >> /sys/fs/cgroup/cgroup.subtree_control
cat /sys/fs/cgroup/cgroup.subtree_control
cpuset cpu memory pids
And indeed i can restart slurmd.
But at the next boot it failed again and /sys/fs/cgroup/cgroup.subtree_control is back with "memory pids" only.
And strangely i found if slurmd is enabled and then i disable it, it change the value of /sys/fs/cgroup/cgroup.subtree_control :
[root@compute ~]# cat /sys/fs/cgroup/cgroup.subtree_control memory pids [root@compute ~]# systemctl disable slurmd Removed /etc/systemd/system/multi-user.target.wants/slurmd.service. [root@compute ~]# cat /sys/fs/cgroup/cgroup.subtree_control cpuset cpu io memory pids
I've made a script at launch time as a dirty fix by using ExecPreStart in slurmd.service:
ExecStartPre=/opt/slurm_bin/dirty_fix_slurmd.sh
with dirty_fix_slurmd.sh:
#!/bin//bash echo "+cpu" >> /sys/fs/cgroup/cgroup.subtree_control echo "+cpuset" >> /sys/fs/cgroup/cgroup.subtree_control echo "+cpu" >> /sys/fs/cgroup/system.slice/cgroup.subtree_control echo "+cpuset" >> /sys/fs/cgroup/system.slice/cgroup.subtree_control
(And i'm not sure if this is something good to do ?)
If you have an idea how to correct this situation
Have a nice day
Thank you
Tristan LEFEBVRE
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Brian Andrus
I'm not sure which specific item to look at, but this seems like
a race condition.
Likely you need to add an override to your slurmd startup
(/etc/systemd/system/slurmd.service/override.conf) and put a
dependency there so it won't start until that is done.
I have mine wait for a few things:
[Unit]
After=autofs.service getty.target sssd.service
That makes it wait for all of those before trying to start.
Brian Andrus
Alan Orth
memory pids
[root@compute ~]# systemctl disable slurmd
Removed /etc/systemd/system/multi-user.target.wants/slurmd.service.
[root@compute ~]# cat /sys/fs/cgroup/cgroup.subtree_control
cpuset cpu io memory pids
Created symlink /etc/systemd/system/multi-user.target.wants/slurmd.service → /usr/lib/systemd/system/slurmd.service.
cpuset cpu io memory pids
Josef Dvoracek via slurm-users
I observe same behavior on slurm 23.11.5 Rocky Linux8.9..
> [root@compute ~]# cat
/sys/fs/cgroup/cgroup.subtree_control
> memory
pids
> [root@compute ~]# systemctl disable slurmd
> Removed
/etc/systemd/system/multi-user.target.wants/slurmd.service.
> [root@compute ~]# cat /sys/fs/cgroup/cgroup.subtree_control
> cpuset cpu io memory pids
> [root@compute ~]# systemctl enable
slurmd
> Created symlink
/etc/systemd/system/multi-user.target.wants/slurmd.service →
/usr/lib/systemd/system/slurmd.service.
> [root@compute ~]# cat /sys/fs/cgroup/cgroup.subtree_control
> cpuset cpu io memory pids
over time (i see this thread is ~1 year old, is here better / new understanding of this?
cheers
josef
Williams, Jenny Avis via slurm-users
There needs to be a slurmstepd infinity process running before slurmd starts.
This doc goes into it:
https://slurm.schedmd.com/cgroup_v2.html
Probably a better way to do this, but this is what we do to deal with that:
::::::::::::::
files/slurm-cgrepair.service
::::::::::::::
[Unit]
Before=slurmd.service slurmctld.service
After=nas-longleaf.mount remote-fs.target system.slice
[Service]
Type=oneshot
ExecStart=/callback/slurm-cgrepair.sh
[Install]
WantedBy=default.target
::::::::::::::
files/slurm-cgrepair.sh
::::::::::::::
#!/bin/bash
/usr/bin/echo +cpu +cpuset +memory >> /sys/fs/cgroup/cgroup.subtree_control && \
/usr/bin/echo +cpu +cpuset +memory >> /sys/fs/cgroup/system.slice/cgroup.subtree_control
/usr/sbin/slurmstepd infinity &
Josef Dvoracek via slurm-users
thanks for hint.
so you end with two "slurmstepd
infinity" processes like me when I tried this workaround?
[root@node ~]#
ps aux | grep slurm
root 1833 0.0 0.0 33716 2188 ? Ss 21:02
0:00 /usr/sbin/slurmstepd infinity
root 2259 0.0 0.0 236796 12108 ? Ss 21:02
0:00 /usr/sbin/slurmd --systemd
root 2331 0.0 0.0 33716 1124 ? S 21:02
0:00 /usr/sbin/slurmstepd infinity
root 2953 0.0 0.0 221944 1092 pts/0 S+ 21:12
0:00 grep --color=auto slurm
[root@node ~]#
Williams, Jenny Avis via slurm-users
The end goal is to see the following 2 things –
jobs under the slurmstepd cgroup path, and
the cpu,cpuset,memory at least in the cgroup.controllers file within the jobs cgroups.controller list.
The pattern you have would be the processes left after boot, first failed slurmd service start which leaves a slurmstepd infinity process, and then the second slurmd starts. In your case there is a second slurmstepd infinity process. As to why those specifics I can’t answer that one sitting here without poking at it more.
Having that slurmstepd infinity running with the cgroups needed ( for us at a minimum cpuset, cpu and memory – YMMV depending on the cgroups.conf settings ) before slurmd tries to start is what enables slurmd to start.
The necessary piece to this working is that the required controls are available at the parent of the path before the slurmd and in particular slurmstepd infinity start.
Our cgroup.conf file is:
CgroupAutomount=yes
ConstrainCores=yes
ConstrainRAMSpace=yes
CgroupPlugin=cgroup/v2
AllowedSwapSpace=1
ConstrainDevices=yes
ConstrainSwapSpace=yes
So the resulting missing piece to get slurmd to start at boot is corrected by running these mods to the cgroup controls before the slurmd service attempts to start. As a test, on your system as it is now without adding anything I’ve mentioned, try having a cgroup.conf with zero Constrain statements. My bet is that in that case slurmd starts clean on boot in that case. I hope that the bug fix does not change slurmd to be more liberal about checking the cgroup control list. – it took a while before I trusted that the controls were actually there so knowing if slurmd starts the controls are there is great.
/usr/bin/echo +cpu +cpuset +memory >> /sys/fs/cgroup/cgroup.subtree_control && \
/usr/bin/echo +cpu +cpuset +memory >> /sys/fs/cgroup/system.slice/cgroup.subtree_control
The job cgroup propagation ( contents of cgroup.controllers files along the cgroup path ) after slurmd + slurmstepd infinity start is via the cgroup path established under slurmstepd.scope . If there is no slurmstepd infinity slurm will start one; if slurmstepd infinity is running and it sets up at minimum the cgroups slurmd needs based on what is in cgroups.con. then slurmd doesn’t end up starting more slurmstepd infinity processes. My recollection is that first slurmstepd infinity does set up the needed cgroup controllers which is why a second slurmd attempt then starts.
To see slurmd complaining about the specifics try disabling slurmd service, reboot, set SLURM_DEBUG_FLAGS = cgroups then run slurmd -D -vvv manually . I am fairly sure that helps see the particulars better.
Theoretically in our setup with the slurm-cgrepair.service we force a slurmstepd infinity process to be running prior* to the slurmd service finishing * ( IDK the PID order says otherwise )
# systemctl show slurmd |egrep cgrepair
After=network-online.target systemd-journald.socket slurm-cgrepair.service remote-fs.target system.slice sysinit.target nvidia.service munge.service basic.target
The resulting behavior of this setup is as we expect – the slurmd service is running on nodes after reboot without intervention. Our steps may not be all necessary, but they are sufficient.
The list of cgroup controllers ( cpu , cpuset, memory for slurmstepd.scope/job_xxxx ) for processes further down the cgoup path can only be a subset of any parent in the cgroup path ( cgroup , cpuset, memory, pid for slurmstepd.scope ).
You asked in the context of what our process tree looks like – here is that information. I add the cgoup field in top for ongoing assurance that user processes are under the slurmstepd.scope path.
This is the process tree on our nodes.
# ps aux |grep slurm |head -n 15 |sed 's/xxxx/aUser/g'
root 8687 0.0 0.0 6471088 34044 ? Ss Apr03 0:29 /usr/sbin/slurmd -D -s
root 8694 0.0 0.0 33668 1080 ? S Apr03 0:00 /usr/sbin/slurmstepd infinity
root 2942928 0.0 0.0 311804 7416 ? Sl Apr06 0:42 slurmstepd: [35400562.extern]
root 2942930 0.0 0.0 311804 7164 ? Sl Apr06 0:43 slurmstepd: [35400563.extern]
root 2942933 0.0 0.0 311804 7144 ? Sl Apr06 0:45 slurmstepd: [35400564.extern]
root 2942935 0.0 0.0 311804 7280 ? Sl Apr06 0:38 slurmstepd: [35400565.extern]
root 2942953 0.0 0.0 312164 7496 ? Sl Apr06 0:45 slurmstepd: [35400564.batch]
root 2942958 0.0 0.0 312164 7620 ? Sl Apr06 0:41 slurmstepd: [35400562.batch]
root 2942960 0.0 0.0 312164 7636 ? Sl Apr06 0:43 slurmstepd: [35400563.batch]
root 2942962 0.0 0.0 312164 7728 ? Sl Apr06 0:41 slurmstepd: [35400565.batch]
aUser 2942972 0.0 0.0 12868 3072 ? SN Apr06 0:00 /bin/bash /var/spool/slurmd/job35400562/slurm_script
aUser 2942973 0.0 0.0 12868 2868 ? SN Apr06 0:00 /bin/bash /var/spool/slurmd/job35400564/slurm_script
aUser 2942974 0.0 0.0 12868 3000 ? SN Apr06 0:00 /bin/bash /var/spool/slurmd/job35400565/slurm_script
aUser 2942975 0.0 0.0 12868 2980 ? SN Apr06 0:00 /bin/bash /var/spool/slurmd/job35400563/slurm_script
root 2944250 0.0 0.0 311804 7248 ? Sl Apr06 0:44 slurmstepd: [35400838.extern]
# pgrep slurm |head -n4 |xargs |sed 's/ /,/g' |xargs -L1 -I{} top -bn1 -Hi -p {}
top - 16:24:16 up 7 days, 21:09, 2 users, load average: 48.07, 47.39, 46.90
Threads: 10 total, 0 running, 10 sleeping, 0 stopped, 0 zombie
%Cpu(s): 76.6 us, 1.1 sy, 1.8 ni, 12.1 id, 7.6 wa, 0.4 hi, 0.4 si, 0.0 st
KiB Mem : 39548588+total, 48296324 free, 28092556 used, 31909702+buff/cache
KiB Swap: 2097148 total, 1354112 free, 743036 used. 32913958+avail Mem
PID USER RES SHR S %CPU %MEM TIME+ P CGROUPS COMMAND
8687 root 34044 7664 S 0.0 0.0 0:04.28 8 0::/system.slice/slurmd.service slurmd
8694 root 1080 936 S 0.0 0.0 0:00.00 46 0::/system.slice/slurmstepd.scope/system slurmstepd
2942928 root 7412 6488 S 0.0 0.0 0:00.01 24 0::/system.slice/slurmstepd.scope/job_35400562/step_extern/slurm slurmstepd
2942936 root 7412 6488 S 0.0 0.0 0:34.29 24 0::/system.slice/slurmstepd.scope/job_35400562/step_extern/slurm `- acctg
2942937 root 7412 6488 S 0.0 0.0 0:08.27 24 0::/system.slice/slurmstepd.scope/job_35400562/step_extern/slurm `- acctg_prof
2942938 root 7412 6488 S 0.0 0.0 0:00.05 24 0::/system.slice/slurmstepd.scope/job_35400562/step_extern/slurm `- slurmstepd
2942930 root 7164 6236 S 0.0 0.0 0:00.01 28 0::/system.slice/slurmstepd.scope/job_35400563/step_extern/slurm slurmstepd
2942939 root 7164 6236 S 0.0 0.0 0:36.40 28 0::/system.slice/slurmstepd.scope/job_35400563/step_extern/slurm `- acctg
2942940 root 7164 6236 S 0.0 0.0 0:07.10 28 0::/system.slice/slurmstepd.scope/job_35400563/step_extern/slurm `- acctg_prof
2942941 root 7164 6236 S 0.0 0.0 0:00.04 28 0::/system.slice/slurmstepd.scope/job_35400563/step_extern/slurm `- slurmstepd
# sacct -j 35400562 -p
JobID|JobName|Partition|Account|AllocCPUS|State|ExitCode|
35400547_10|run_s111.sh|general|slurm_account|1|RUNNING|0:0|
35400547_10.batch|batch||slurm_account|1|RUNNING|0:0|
35400547_10.extern|extern||slurm_account|1|RUNNING|0:0|
# scontrol listpids 35400562
PID JOBID STEPID LOCALID GLOBALID
-1 35400562 extern 0 0
2942928 35400562 extern - -
2942946 35400562 extern - -
2942972 35400562 batch 0 0
2942958 35400562 batch - -
2943039 35400562 batch - -
# cat /sys/fs/cgroup/system.slice/slurmstepd.scope/cgroup.controllers
cpuset cpu memory pids
# cat /sys/fs/cgroup/system.slice/slurmstepd.scope/job_35400562/step_extern/slurm/cgroup.controllers
cpuset cpu memory