Thank you Hemann and Tom! That was it.
The new cluster has a virtual memory limit on the login host, and the
old cluster did not.
It doesn't look like there is any way to set a default to override the
srun behaviour of passing those resource limits to the shell, so I may
consider removing those limits on the login host so folks don't have to
manually specify this every time.
I really appreciate the help!
-Dj
On 5/15/24 07:20, greent10--- via slurm-users wrote:
Hi,
When we first migrated to Slurm from PBS one of the strangest issues we hit was
that ulimit settings are inherited from the submission host which could explain
the different between ssh'ing into the machine (and the default ulimit being
applied) and with running a job via srun.
You could use:
srun --propagate=NONE --mem=32G --pty bash
I still find Slurm inheriting ulimit and environment variables from the
submission host an odd default behaviour.
Tom
--
Thomas Green Senior Programmer
ARCCA, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB
Tel: +44 (0)29 208 79269 Fax: +44 (0)29 208 70734
Email: green...@cardiff.ac.uk Web: http://www.cardiff.ac.uk/arcca
Thomas Green Uwch Raglennydd
ARCCA, Adeilad Redwood, King Edward VII Avenue, Caerdydd, CF10 3NB
Ffôn: +44 (0)29 208 79269 Ffacs: +44 (0)29 208 70734
E-bost: green...@caerdydd.ac.uk Gwefan: http://www.caerdydd.ac.uk/arcca
-----Original Message-----
From: Hermann Schwärzler via slurm-users <slurm-users@lists.schedmd.com>
Sent: Wednesday, May 15, 2024 9:45 AM
To: slurm-users@lists.schedmd.com
Subject: [slurm-users] Re: srun weirdness
External email to Cardiff University - Take care when replying/opening
attachments or links.
Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor
atodiadau neu ddolenni.
Hi Dj,
could be a memory-limits related problem. What is the output of
ulimit -l -m -v -s
in both interactive job-shells?
You are using cgroups-v1 now, right?
In that case what is the respective content of
/sys/fs/cgroup/memory/slurm_*/uid_$(id -u)/job_*/memory.limit_in_bytes
in both shells?
Regards,
Hemann
On 5/14/24 20:38, Dj Merrill via slurm-users wrote:
I'm running into a strange issue and I'm hoping another set of brains
looking at this might help. I would appreciate any feedback.
I have two Slurm Clusters. The first cluster is running Slurm 21.08.8
on Rocky Linux 8.9 machines. The second cluster is running Slurm
23.11.6 on Rocky Linux 9.4 machines.
This works perfectly fine on the first cluster:
$ srun --mem=32G --pty /bin/bash
srun: job 93911 queued and waiting for resources
srun: job 93911 has been allocated resources
and on the resulting shell on the compute node:
$ /mnt/local/ollama/ollama help
and the ollama help message appears as expected.
However, on the second cluster:
$ srun --mem=32G --pty /bin/bash
srun: job 3 queued and waiting for resources
srun: job 3 has been allocated resources
and on the resulting shell on the compute node:
$ /mnt/local/ollama/ollama help
fatal error: failed to reserve page summary memory runtime stack:
runtime.throw({0x1240c66?, 0x154fa39a1008?})
runtime/panic.go:1023 +0x5c fp=0x7ffe6be32648 sp=0x7ffe6be32618
pc=0x4605dc runtime.(*pageAlloc).sysInit(0x127b47e8, 0xf8?)
runtime/mpagealloc_64bit.go:81 +0x11c fp=0x7ffe6be326b8
sp=0x7ffe6be32648 pc=0x456b7c
runtime.(*pageAlloc).init(0x127b47e8, 0x127b47e0, 0x128d88f8, 0x0)
runtime/mpagealloc.go:320 +0x85 fp=0x7ffe6be326e8
sp=0x7ffe6be326b8
pc=0x454565
runtime.(*mheap).init(0x127b47e0)
runtime/mheap.go:769 +0x165 fp=0x7ffe6be32720 sp=0x7ffe6be326e8
pc=0x451885
runtime.mallocinit()
runtime/malloc.go:454 +0xd7 fp=0x7ffe6be32758 sp=0x7ffe6be32720
pc=0x434f97
runtime.schedinit()
runtime/proc.go:785 +0xb7 fp=0x7ffe6be327d0 sp=0x7ffe6be32758
pc=0x464397
runtime.rt0_go()
runtime/asm_amd64.s:349 +0x11c fp=0x7ffe6be327d8
sp=0x7ffe6be327d0 pc=0x49421c
If I ssh directly to the same node on that second cluster (skipping
Slurm entirely), and run the same "/mnt/local/ollama/ollama help"
command, it works perfectly fine.
My first thought was that it might be related to cgroups. I switched
the second cluster from cgroups v2 to v1 and tried again, no
difference. I tried disabling cgroups on the second cluster by
removing all cgroups references in the slurm.conf file but that also
made no difference.
My guess is something changed with regards to srun between these two
Slurm versions, but I'm not sure what.
Any thoughts on what might be happening and/or a way to get this to
work on the second cluster? Essentially I need a way to request an
interactive shell through Slurm that is associated with the requested
resources. Should we be using something other than srun for this?
Thank you,
-Dj
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