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snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
18 stars 19 forks source link

feat: in job stability #137

Closed cmeesters closed 3 months ago

cmeesters commented 3 months ago

might increase stability of in-job submissions, might fix #113

Summary by CodeRabbit

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Commits Files that changed from the base of the PR and between 5a12e61adb55dffce08d7a6ef06cf0800c957e44 and 6f0482c371bcd7209da2c35e615cebaf2385d9bd.

Walkthrough

The updates include the addition of a utility function, delete_slurm_environment, to manage SLURM-related environment variables, enhancing resource management. The warn_on_jobcontext method in the ExecutorSettings class has been modified to call this utility function when a warning about running Snakemake in a SLURM context is logged. This aims to ensure a cleaner execution environment for jobs.

Changes

Files Change Summary
snakemake_executor_plugin_slurm/__init__.py
snakemake_executor_plugin_slurm/utils.py		 Added the delete_slurm_environment function to unset SLURM-related environment variables and modified warn_on_jobcontext to call this function when logging a warning.

Assessment against linked issues

Objective Addressed Explanation
Properly handle SLURM job context warnings (#113) ✅
Ensure environment cleanliness for SLURM jobs (#113) ✅
Improve Snakemake compatibility when run under SLURM (#113) ❓ The changes address warnings but may not fully resolve compatibility issues.

Poem

In the meadow where bunnies hop,
SLURM jobs run without a stop.
With a cleanup dance, we twirl and cheer,
No lingering vars, we have no fear!
Snakemake's path is now so bright,
Hopping along, everything feels right! 🐇✨

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cmeesters commented 3 months ago

@fgvieira would you have time to review this PR? Alas, we cannot test this within the CI (due to lack of resources). Seems to work fine for me and others.

fgvieira commented 3 months ago

Why is it not recommended to run snakemake as a SLURM job? That is how I've been running it.

cmeesters commented 3 months ago

Thing is: The executor exports the environment. This has to be done, because otherwise the base environment might not be present. Within a SLURM job the SLURM_* got exported, too. This caused SLURM in some cases to complain about mem and mem_per_cpu mismatches.

I am not sure the current PR will fix all issues. I am even not sure, that 100 % stability can be achieved at all - apparently HPC admins made akward configuration a hobby ... But removing the scheduler env variables certainly is a step forward.

fgvieira commented 3 months ago

So the idea would be to remove all SLURM_* env variables from the (new) launched job. Not the parent snakemake job, right?

cmeesters commented 3 months ago

In fact, you cannot remove environment variables from a parent shell. Hence, python can only remove within the current environment on a node, not its jobscript. Within the Snakemake process on that node, you would not see the SLURM_* variables any more. Also, a daughter process of the same Python process would not be able to see them. A newly lauchned job (on the same node or a different one) would get a fresh population of SLURM_* env variables by SLURM itself.

If you use (host based) logins to that node, you too do not see these environment variables (because: new shell). Howver, if your run 

$ srun -A <account> -p <partition> --pty -t 10 bash -i
<node>:<path>$ python3
>>> import os
>>> print(os.environ["SLURM_JOB_ID"])
376803
>>> del os.environ["SLURM_JOB_ID"]
>>> print(os.environ["SLURM_JOB_ID"])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<frozen os>", line 714, in __getitem__
KeyError: 'SLURM_JOB_ID'
>>> 
<node>:<path>$ echo $SLURM_JOB_ID
376803

you will see, that you are able to tinker with env vars within your process, not in the parent shell.