nextflow-io / nextflow-io/nextflow
exitStatusReadTimeoutMillis
Nobody has claimed this yet.
- Dominant language
- Groovy
- Stars
- 3.5k
- Forks
- 811
- Avg merge
- 2d 11h
- Merged PRs (30d)
- 61
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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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