nextflow-io / nextflow-io/nextflow

Please allow Nextflow to monitor the disk space of a process and optionally kill it if a certain amount of disk space is reached

Open
#4,785 1 comment 2 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

stale
Dominant language
Groovy
Stars
3.5k
Forks
811
Avg merge
2d 11h
Merged PRs (30d)
61

Description

New feature

Hi! Thanks for using Nextflow and submitting the proposal
for a new feature or the enhancement of an existing functionality.

Please replace this text providing a short description of your
proposal.

Usage scenario

If a process, or several processes of potentially different users run on an HPC node with limited disk space, it is important to monitor how much disk space each process occupies. Or else a process might get killed by the scheduler and Nextflow is not giving any hints what so ever why this is happening. It is a pain on the admin side to debug such a problem. For more details please see https://nextflow.slack.com/archives/C02T98A23U7/p1709196894689059.

Suggest implementation

Add a new param type like max_disk_usage to any config file which tells a process or a HPC in general how much disk space can be occupied.

In the past, Nextflow jobs were killed randomly and it took us days to find out why, because there were no logs or error messages. Monitoring the disk space occupied and killing a process early might be of help here.

Thanks!

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

The issue names no files, tests, or entry points, so first identify where process configuration and HPC execution are handled. Define how disk usage is measured, configured, reported, and enforced for individual or shared processes; done means the behavior is specified, implemented, and covered by tests.

Written by the indexing model from the issue text.

Assessment

Tech stack
groovy
Domain
hpc
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.