Effectively use batchtools for Targets-based workflow in SLURM

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#292 4 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
r
Domain
hpc

Research direction

Start by reading the issue and the linked targets discussion, then investigate how failed SLURM jobs, including memory overflows and timeouts, are reported to batchtools. Reproduce the behavior with a representative targets workflow; done means failed jobs are communicated correctly instead of remaining marked as executing.

Written by the indexing model from the issue text.

Description

Thanks for the great package.

We are converting a makeflow workflow to R using targets + batchtools, for a SLURM system.

However, we find practically unusable because the job that fail do not communicate to batchtools that thinks are still executing. They might fail for memory overflow or timeout.

Please see https://github.com/ropensci/targets/discussions/932

Are you aware of these limitations and do you know a way to solve this?

Dominant language
R
Stars
184
Forks
53
Avg merge
7d 2h
Merged PRs (30d)
1

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Open the contributing guide

First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

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