nextflow-io / nextflow-io/nextflow
If memory is specified, tasks will not run on the UGE engine
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Description
Bug report
Parameters in config h_rt/h_rss/mem_free should not be specified by Nextflow.
This is because some supercomputers are unable to accept these parameters. I am not sure if this is common or not.
However, at least on NIG supercomputer system( https://sc.ddbj.nig.ac.jp/ ), ques never run.
We need to use h_vmem instead of those parameters.
https://nfcore.slack.com/archives/CGRTMASKY/p1629489188025100
I solved the problem by this conversation's methods.
In config file
memory = null
Is there any way to replace this, for example by creating a new option?
Null sometimes causes errors in downstream workflows.
Expected behavior and actual behavior
Ques run immediately.
Ques never run.
Steps to reproduce the problem
Not works.
- memory = '16G'
- memory was not specified
Works - memory = null
Environment
- Nextflow version: 21.04.3
- Java version: 11
- Operating system: CentOS7.5
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 by tracing the UGE engine's handling of the h_rt, h_rss, mem_free, h_vmem, and memory configuration mentioned in the report. Reproduce the difference between memory='16G', an omitted memory setting, and memory=null on the stated environment, then verify that a supported configuration lets queued tasks run without introducing downstream null errors.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- groovy
- Domain
- hpc
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100