[slurm-users] Troubles with cgroups
jsimms1 at swarthmore.edu
Tue Mar 21 16:42:08 UTC 2023
Thanks for following up about this. What you say makes sense: at Lafayette,
we didn't experience the issue until upgrading to a Slurm version that
supported cgroups/v2, and here at Swarthmore, we are still on a version of
Slurm that doesn't and we don't have the issue (both Rocky 8). At this
point I'm still intending to disable swap entirely during our next
maintenance cycle, but if we can identify the issue and a
reasonable solution, perhaps we don't have to.
Please keep us posted on how your testing goes! It would be great to
confirm that it's a reproducible bug and not something related to our
hardware or configuration.
On Tue, Mar 21, 2023 at 12:19 PM Hermann Schwärzler <
hermann.schwaerzler at uibk.ac.at> wrote:
> Hi Jason,
> thank you for your reply.
> From what I can tell your problem *is* the same as ours. BTW: we were
> already talking about disabling swap in our nodes as a last resort. :-)
> In the meantime we made some new findings: we can trigger the error when
> (with cgroups/v2) we set memory.high and memory.max to the same value
> (as Slurm does it in our configuration). And this error occurs with
> Rocky Linux 8.x as well as with 9.x.
> It does *not* get triggered when memory.high is set to the limit and
> memory.max is set to some higher value or "max".
> Our plans are now to check if this is also happening in RHEL. If yes we
> will open a support case.
> And if time permits we will check if it can be triggered with a vanilla
> On 3/17/23 21:34, Jason Simms wrote:
> > Hello,
> > This isn't precisely related, but I can say that we were having strange
> > issues with system load spiking to the point that the nodes became
> > unresponsive and likewise needed a hard reboot. After several tests and
> > working with our vendor, on nodes that we entirely disabled swap, the
> > problems ceased. You may have an absolutely valid need for swap, or some
> > configurations may in fact rely on it for whatever reason, but for now
> > we've chosen to disable swap on all nodes. It's interesting, however,
> > because I didn't really identify the culprit, and it may be related to
> > cgroups somehow, but regardless, disabling swap appears to be working
> > for us with no immediate consequences.
> > Warmest regards,
> > Jason
> > On Thu, Mar 16, 2023 at 10:59 AM Hermann Schwärzler
> > <hermann.schwaerzler at uibk.ac.at <mailto:hermann.schwaerzler at uibk.ac.at>>
> > wrote:
> > Dear Slurm users,
> > after opening our new cluster (62 nodes - 250 GB RAM, 64 cores each -
> > Rocky Linux 8.6 - Kernel 4.18.0-372.16.1.el8_6.0.1 - Slurm 22.05) for
> > "friendly user" test operation about 6 weeks ago we were soon facing
> > serious problems with nodes that suddenly become unresponsive (so
> > so that only a hard reboot via IPMI gets them back).
> > We were able to narrow the problem down to one similar to this one:
> > https://github.com/apptainer/singularity/issues/5850
> > <https://github.com/apptainer/singularity/issues/5850>
> > Although in our case it's not related to Singularity but generally to
> > cgroups.
> > We are using cgroups in our Slurm configuration to limit RAM, CPUs
> > devices. In the beginning we did *not* limit swap space (we are
> > doing so
> > now to work around the problem but would like to allow at least some
> > swap space).
> > We are able to reproduce the problem *outside* Slurm as well by using
> > the small test program mentioned in the above Singularity
> > (https://gist.github.com/pja237/b0e9a49be64a20ad1af905305487d41a
> > <https://gist.github.com/pja237/b0e9a49be64a20ad1af905305487d41a>)
> > these steps (for cgroups/v1):
> > cd /sys/fs/cgroup/memory
> > mkdir test
> > cd test
> > echo $((5*1024*1024*1024)) > memory.limit_in_bytes
> > echo $$ > cgroup.procs
> > /path/to/mempoc 2 10
> > After about 10 to 30 minutes the problem occurs.
> > We tried to switch to cgroups/v2. Which does solve the problem for
> > manual case outside Slurm:
> > cd /sys/fs/cgroup
> > mkdir test
> > cd test
> > echo "+memory" > cgroup.subtree_control
> > mkdir test2
> > echo $((5*1024*1024*1024)) > test2/memory.high
> > echo $$ > test2/cgroup.procs
> > /path/to/mempoc 2 10
> > Now it runs for days and weeks without any issues!
> > But when we run the same thing in Slurm (with cgroups/v2 configured
> > *not limit* swapping) by using
> > sbatch --mem=5G --cpus-per-task=10 \
> > --wrap "/path/to/mempoc 2 10"
> > the nodes still become unusable after some time (1 to 5 hours) with
> > usual symptoms.
> > Did anyone of you face similar issues?
> > Are we missing something?
> > Is it unreasonable to think our systems should stay stable even when
> > there is cgroup-based swapping?
> > Kind regards,
> > Hermann
> > --
> > *Jason L. Simms, Ph.D., M.P.H.*
> > Manager of Research Computing
> > Swarthmore College
> > Information Technology Services
> > (610) 328-8102
> > Schedule a meeting: https://calendly.com/jlsimms
> > <https://calendly.com/jlsimms>
*Jason L. Simms, Ph.D., M.P.H.*
Manager of Research Computing
Information Technology Services
Schedule a meeting: https://calendly.com/jlsimms
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