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jean-zay-users / jean-zay-doc

Collaborative documentation for and from Jean Zay users. Official Jean Zay documentation: http://www.idris.fr/eng/jean-zay/
https://jean-zay-doc.readthedocs.io/en/latest/
MIT License
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WORK inodes limitations / troubleshooting / work-arounds #69

Open lesteve opened 3 years ago

lesteve commented 3 years ago

From https://gitter.im/jean-zay-users/jean-zay-doc?at=60ae90153d43a15a65c9fad0

High-level overview (quick to run <1s, but the info may be stale, it is refreshed periodically IIRC). It also tells you your inodes quota:

idrquota -w

Exact method to count the inodes in some folder but slower (a few seconds), -d1 is to get the info about one-level deep folders:

du -d1 --inodes $WORK

In practice, the main limitation happens if you have a miniconda install in the WORK. If that's the case conda clean -tipy may remove some unused files and save you some inodes.

Feel free to comment if you have additional tips and tricks!

You can ask to increase your inodes quota, but it seems like there is a special procedure that I don't know about ... maybe @guhur you can add some info here if you manage to do it 😉

lesteve commented 3 years ago

For the conda environment use case, I am thinking maybe there is a convenient way to use conda-pack to create .tar.gz or even .squashfs that use a single inode and then you can untar this in the SCRATCH.

This is not as convenient as having a conda environment always accessible but maybe an OK work-around?

With the squashfs option there maybe an easy way to use it without unpacking, I need to ask user support about this, I think at one point they said it is supported on Jean-Zay.

RemiLacroix-IDRIS commented 3 years ago

With the squashfs option there maybe an easy way to use it without unpacking

It should be possible but as far as I can tell conda-pack does not support SquashFS natively.

lesteve commented 3 years ago

It does actually but for some reason their doc website is not up-to-date ... look at one of the last commit 😉

lesteve commented 3 years ago

There you go: https://github.com/conda/conda-pack/pull/177/files

@RemiLacroix-IDRIS by the way, since you are here, it would be great if you can post the way to mount a squashfs image on Jean-Zay (if I remember correctly you can even do this without singularity).

RemiLacroix-IDRIS commented 3 years ago

It does actually but for some reason their doc website is not up-to-date ... look at one of the last commit wink

This is indeed really new, it's probably not in an official release yet hence not in the doc on the website.

it would be great if you can post the way to mount a squashfs image on Jean-Zay

This feature is still in beta stage but I will let you know as soon as we release it.

lesteve commented 3 years ago

This is indeed really new, it's probably not in an official release yet hence not in the doc on the website.

In Python open-source (especially true for small projects) this is often the case that doc is built from the master branch but not in this case indeed, they deploy the doc only for tags: https://github.com/conda/conda-pack/blob/0bdd462691e8dc31edb0dcdb86a332cc6ddaeda9/.github/workflows/main.yml#L155-L160

lesteve commented 3 years ago

it would be great if you can post the way to mount a squashfs image on Jean-Zay

This feature is still in beta stage but I will let you know as soon as we release it.

Ah OK I thought it was already possible, let me know if I can help for beta-testing 😉