nextflow-io / nextflow-io/nextflow
Google Batch: Setting `accelerator` directive removes docker ENTRYPOINT instructions
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- Dominant language
- Groovy
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Description
Bug report
As the title says, if somebody provides "accelerator" to the configuration of a process, the container of that process does not start with the pre-defined entrypoint from the dockerfile it was built from.
A "minimal" example:
entrypoint.sh:
echo "hello world"
bash $@
Dockerfile:
FROM python:3.13-slim
# Setting up home
ENV HOME=/home/root
WORKDIR /home/root
RUN chmod 777 /home/root
COPY entrypoint.sh /home/root/entrypoint.sh
ENTRYPOINT ["/home/root/entrypoint.sh"]
Build the container and push it to Artifact Registry, say to CONTAINER_URI
example.nf:
processAc {
container: CONTAINER_URI
accelerator: [limit: 1, type: 'nvidia-tesla-t4']
script:
"""
exit 0
"""
}
processWoAc {
container: CONTAINER_URI
script:
"""
exit 0
"""
}
workflow {
processAc()
processWoAc()
}
The google batch logs of processWoAc task will show the "hello world" message, but not for processAc task.
Environment
- Nextflow version: 26.04.4
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
Reproduce the behavior using entrypoint.sh, the Dockerfile, and example.nf, then compare the Google Batch logs for processAc and processWoAc. Trace how the accelerator setting changes container startup; done means the accelerator task also runs the Dockerfile ENTRYPOINT and prints the expected "hello world" message.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, google-cloud
- Domain
- cloud, devops
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100