[slurm-users] Wedged nodes from cgroups, OOM killer, and D state process

[Christopher Benjamin Coffey]

Hi,

We've been noticing an issue with nodes from time to time that become "wedged", or unusable. This is a state where ps, and w hang. We've been looking into this for a while when we get time and finally put some more effort into it yesterday. We came across this blog which describes almost the exact scenario:

https://rachelbythebay.com/w/2014/10/27/ps/

It has nothing to do with Slurm, but it does have to do with cgroups which we have enabled. It appears that processes that have hit their ceiling for memory and should be killed by oom-killer, and are in D state at the same time, cause the system to become wedged. For each node wedged, I've found a job out in:

/cgroup/memory/slurm/uid_3665/job_15363106/step_batch
- memory.max_usage_in_bytes
- memory.limit_in_bytes

The two files are the same bytes, which I'd think would be a candidate for oom-killer. But memory.oom_control says:

oom_kill_disable 0
under_oom 0

My feeling is that the process was in D state, the oom-killer tried to be invoked, but then didn't and the system became wedged.

Has anyone run into this? If so, whats the fix? Apologies if this has been discussed before, I haven't noticed it on the group.

I wonder if it’s a bug in the oom-killer? Maybe it's been patched in a more recent kernel but looking at the kernels in the 6.10 series it doesn't look like a newer one would have a patch for a oom-killer bug.

Our setup is:

Centos 6.10
2.6.32-642.6.2.el6.x86_64
Slurm 17.11.12

And /etc/slurm/cgroup.conf
ConstrainCores=yes
ConstrainRAMSpace=yes
ConstrainSwapSpace=yes

Cheers,
Chris

—
Christopher Coffey
High-Performance Computing
Northern Arizona University
928-523-1167