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exitStatusReadTimeoutMillis #5813

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machine-moon opened this issue Feb 24, 2025 · 0 comments
Open

exitStatusReadTimeoutMillis #5813

machine-moon opened this issue Feb 24, 2025 · 0 comments

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@machine-moon
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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.
#2672
#1045

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