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Preempted Job Causes Workflow Manager Hard Failure

SLURM reclaimed the node for a higher-priority job and sent a SIGTERM. The running application did not catch the signal to gracefully exit or checkpoint within the 2-minute grace period. The workflow manager was not configured to interpret the 'PREEMPTED' (PR) state as a resumable event.

Quick answer

SLURM reclaimed the node for a higher-priority job and sent a SIGTERM.

Symptom
Workflow manager error: Job failed with exit code 15
Root cause
SLURM reclaimed the node for a higher-priority job and sent a SIGTERM. The running application did not catch the signal to gracefully exit or checkpoint within the 2-minute grace period. The workflow manager was not configured to interpret the 'PREEMPTED' (PR) state as a resumable event.
Recommended fix
errorStrategy = { task.exitStatus == 15 ? 'retry' : 'terminate' }
How Denpex helps
Denpex matches Preempted Job Causes Workflow Manager Hard Failure across every rank in a distributed run and reports which rank failed first, so you act on the initiating node instead of the loudest one.
Job Execution#Preemption Handling

What this failure is

Preempted Job Causes Workflow Manager Hard Failure is a Job Execution failure seen during ML training runs. SLURM reclaimed the node for a higher-priority job and sent a SIGTERM. The running application did not catch the signal to gracefully exit or checkpoint within the 2-minute grace period. The workflow manager was not configured to interpret the 'PREEMPTED' (PR) state as a resumable event. Common tags: Preemption Handling.

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Why it happens (the mechanism)

The application logs just show it was killed or exited with code 15, appearing as an unexpected crash or OOM, when it was actually a routine scheduler preemption.

What you'll observe

  • slurmstepd: error: *** JOB <ID> ON <node> CANCELLED AT <time> DUE TO PREEMPTION ***
  • Workflow manager error: Job failed with exit code 15

Common symptoms and what they mean

SymptomWhy it happens
A long-running machine learning job is killed abruptly.SLURM reclaimed the node for a higher-priority job and sent a SIGTERM. The running application did not catch the signal to gracefully exit or checkpoint within the 2-minute grace period. The workflow manager was not configured to interpret the 'PREEMPTED' (PR) state as a resumable event.
The workflow manager (e.g. Nextflow) marks the task as failed and aborts the entire pipeline instead of resubmitting.SLURM reclaimed the node for a higher-priority job and sent a SIGTERM. The running application did not catch the signal to gracefully exit or checkpoint within the 2-minute grace period. The workflow manager was not configured to interpret the 'PREEMPTED' (PR) state as a resumable event.

Which systems are affected

  • SLURM
  • Snakemake
  • Nextflow

How to confirm this is the problem

Use this checklist to test the hypothesis against a small reproduction. No single line proves the root cause, so preserve the preceding events and compare one variable at a time.

  • Run `sacct -j <job_id> -o State,Reason` and look for the 'PREEMPTED' state.
  • Check application logs for received signals (SIGTERM).

Searchable error signature

search key
Workflow manager error: Job failed with exit code 15
slurmstepd: error: *** JOB <ID> ON <node> CANCELLED AT <time> DUE TO PREEMPTION ***

Use this text as a lookup key in logs and upstream issue trackers. It is not presented as a captured customer log. Confirm the cause from your own preceding events, versions, configuration and the cited references.

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Root cause

  • SLURM reclaimed the node for a higher-priority job and sent a SIGTERM. The running application did not catch the signal to gracefully exit or checkpoint within the 2-minute grace period. The workflow manager was not configured to interpret the 'PREEMPTED' (PR) state as a resumable event.

The fix and how to prevent it

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