nextflow-io / nextflow-io/nextflow

exitStatusReadTimeoutMillis

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executor/slurm
Dominant language
Groovy
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Description

Bug report

Expected behavior and actual behavior

I expect the pipeline to run, but its requesting a error code and times out after 4.5 minutes while my pipeline is still running, even if i try a retry strat or anything, the pipeline is STILL executing in the background..

Steps to reproduce the problem

nextflow run myworkflow.nf

Program output

ERROR ~ Error executing process > 'TASK2'

Caused by:
Process TASK2 terminated for an unknown reason -- Likely it has been terminated by the external system

Command exit status:

Command output:
(empty)

Feb-24 18:41:30.804 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[jobId: 2998128; id: 2; name: TASK2; status: RUNNING; exit: -; error: -; workDir: [/path/to]/work/b4/9b7db98b055639f6058494719b451e started: 1740422190792; exited: -; ]
Feb-24 18:43:30.814 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 2998128; id: 2; name: TASK2; status: RUNNING; exit: -; error: -; workDir: [/path/to]/work/b4/9b7db98b055639f6058494719b451e started: 1740422190792; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270020
Current queue status:
>   (empty)
Environment
  • Nextflow version: [?]
  • Java version:
    openjdk 11.0.26 2025-01-21
    OpenJDK Runtime Environment (build 11.0.26+4-post-Ubuntu-1ubuntu122.04)
    OpenJDK 64-Bit Server VM (build 11.0.26+4-post-Ubuntu-1ubuntu122.04, mixed mode, sharing)
  • Operating system: [macOS, Linux, etc]
    LSB Version: core-11.1.0ubuntu4-noarch:printing-11.1.0ubuntu4-noarch:security-11.1.0ubuntu4-noarch
    Distributor ID: Ubuntu
    Description: Ubuntu 22.04.5 LTS
    Release: 22.04
    Codename: jammy
  • Bash version: (use the command $SHELL --version)
    GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)
Additional context

running on SLURM.
Similar to these issues.
https://github.com/nextflow-io/nextflow/issues/2672
https://github.com/nextflow-io/nextflow/issues/1045

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the SLURM executor path around GridTaskHandler and the exitStatusReadTimeoutMillis message shown in the report. Reproduce the issue with the provided nextflow run command and a long-running SLURM task; done means a still-running task is not reported as failed while its exit status is being checked.

Written by the indexing model from the issue text.

Assessment

Tech stack
groovy
Domain
hpc, infrastructure
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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