feat: treat sbatch errors as job errors instead of workflow errors #322

nikostr · 2025-06-09T10:22:03Z

This PR is a potential solution to #320. When I do some very rudimentary testing it seems to work: when sbatch fails, it is handled like a job error rather than a workflow error.

The argument for report_job_error needs to be a SubmittedJobInfo. These jobs are technically never reported as submitted. I'm not sure if that would cause some type of problem? Would this PR need some sort of tests included?

Summary by CodeRabbit

Bug Fixes
- Improved error handling during SLURM job submission to prevent unnecessary interruptions when an error occurs, ensuring smoother workflow execution.

coderabbitai · 2025-06-09T10:22:10Z

Walkthrough

The change updates the error handling in the run_job method of the SLURM executor plugin. When a subprocess.CalledProcessError occurs during job submission, the method now reports the job error and returns instead of raising an exception, except when the error output contains "submission failed," which still raises a WorkflowError.

Changes

File(s)	Change Summary
snakemake_executor_plugin_slurm/init.py	Modified error handling in `run_job`: now reports job error and returns on `CalledProcessError`, except for specific failure messages.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant SLURMExecutor
    participant SLURM (sbatch)

    User->>SLURMExecutor: run_job()
    SLURMExecutor->>SLURM: Execute sbatch command
    alt sbatch succeeds
        SLURM-->>SLURMExecutor: Success response
        SLURMExecutor-->>User: Continue workflow
    else sbatch fails (CalledProcessError)
        SLURM-->>SLURMExecutor: Error output
        alt error output contains "submission failed"
            SLURMExecutor-->>User: Raise WorkflowError
        else other error
            SLURMExecutor->>SLURMExecutor: report_job_error()
            SLURMExecutor-->>User: Return (suppress exception)
        end
    end

Possibly related PRs

fix: logfile quoting and scancel error handling #140: Both PRs adjust error handling for subprocess exceptions in SLURM job submission within run_job.
fix: sbatch stderr parsing #2 #165: Both PRs refine how submission errors from the SLURM sbatch command are detected and reported in run_job.
fix: sbatch stderr parsing #161: Both PRs focus on processing and reporting subprocess errors during SLURM job submission in the executor plugin.

Suggested reviewers

johanneskoester
fgvieira

Poem

A job was sent, but trouble came—
The SLURM command refused the game.
Now errors are gently caught,
Reported swiftly, workflow not distraught.
With careful paws, the code now flows,
The rabbit hops—no fatal throws! 🐇

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Actionable comments posted: 1

📜 Review details

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Reviewing files that changed from the base of the PR and between ec82a70 and 3170182.

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🧰 Additional context used

🧠 Learnings (1)

snakemake_executor_plugin_slurm/__init__.py (1)

Learnt from: cmeesters
PR: snakemake/snakemake-executor-plugin-slurm#178
File: snakemake_executor_plugin_slurm/__init__.py:0-0
Timestamp: 2024-12-11T14:17:08.749Z
Learning: In the `snakemake-executor-plugin-slurm` project, when handling exceptions in `snakemake_executor_plugin_slurm/__init__.py`, prefer concise error messages and avoid unnecessary verbosity or exception chaining when it's not necessary.

snakemake_executor_plugin_slurm/__init__.py

nikostr · 2025-06-09T12:28:06Z

The msg currently shows up in the message of the first report of the rule error, but only None is shown as message for the final display of errors. I'm not sure what's up with that, but this seems to happen independent of this PR, and even independent of SLURM(?). Either way, it could probably be formatted in a nicer way.

nikostr added 2 commits June 9, 2025 11:14

fix: replace WorkflowError with report_job_error for sbatch failure

a0d47ef

fix: wrap job in SubmittedJobInfo when calling report_job_error

3170182

nikostr mentioned this pull request Jun 9, 2025

SLURM sbatch failed causes Snakemake crash #320

Open

nikostr changed the title ~~Treat sbatch errors as job errors instead of workflow errors~~ feat: treat sbatch errors as job errors instead of workflow errors Jun 9, 2025

coderabbitai bot reviewed Jun 9, 2025

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snakemake_executor_plugin_slurm/__init__.py Outdated Show resolved Hide resolved

nikostr added 2 commits June 9, 2025 12:51

Add error message when reporting jobs failed due to bad sbatch call

3553b13

Improve readability of error msg for bad sbatch jobs

87fb93c

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