[slurm-users] Jobs killed by OOM-killer only on certain nodes.
novosirj at rutgers.edu
Thu Jul 2 14:20:38 UTC 2020
Are you sure that the OOM killer is involved? I can get you specifics later, but if it’s that one line about OOM events, you may see it after successful jobs too. I just had a SLURM bug where this came up.
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On Jul 2, 2020, at 09:53, Prentice Bisbal <pbisbal at pppl.gov> wrote:
I maintain a very heterogeneous cluster (different processors, different amounts of RAM, etc.) I have a user reporting the following problem.
He's running the same job multiple times with different input parameters. The jobs run fine unless they land on specific nodes. He's specifying --mem=2G in his sbatch files. On the nodes where the jobs fail, I see that the OOM killer is invoked, so I asked him to specify more RAM, so he did. He set --mem=4G, and still the jobs fail on these 2 nodes. However, they run just fine on other nodes with --mem=2G.
When I look at the slurm log file on the nodes, I see something like this for a failing job (in this case, --mem=4G was set)
[2020-07-01T16:19:06.222] _run_prolog: prolog with lock for job 801777 ran for 0 seconds
[2020-07-01T16:19:06.479] [801777.extern] task/cgroup: /slurm/uid_40324/job_801777: alloc=4096MB mem.limit=4096MB memsw.limit=unlimited
[2020-07-01T16:19:06.483] [801777.extern] task/cgroup: /slurm/uid_40324/job_801777/step_extern: alloc=4096MB mem.limit=4096MB memsw.limit=unlimited
[2020-07-01T16:19:06.506] Launching batch job 801777 for UID 40324
[2020-07-01T16:19:06.621] [801777.batch] task/cgroup: /slurm/uid_40324/job_801777: alloc=4096MB mem.limit=4096MB memsw.limit=unlimited
[2020-07-01T16:19:06.623] [801777.batch] task/cgroup: /slurm/uid_40324/job_801777/step_batch: alloc=4096MB mem.limit=4096MB memsw.limit=unlimited
[2020-07-01T16:19:19.385] [801777.batch] sending REQUEST_COMPLETE_BATCH_SCRIPT, error:0 status:0
[2020-07-01T16:19:19.389] [801777.batch] done with job
[2020-07-01T16:19:19.463] [801777.extern] _oom_event_monitor: oom-kill event count: 1
[2020-07-01T16:19:19.508] [801777.extern] done with job
Any ideas why the jobs are failing on just these two nodes, while they run just fine on many other nodes?
For now, the user is excluding these two nodes using the -x option to sbatch, but I'd really like to understand what's going on here.
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