Cellpose update: 3.0.1 --> 3.1.0

[kbestak]

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Changes: https://github.com/MouseLand/cellpose/releases/tag/v3.1.0

[kbestak]

Hi Biocontainers team,
I have two questions connected to the PR above:

1. What would be the best way to add GPU acceleration support to the container? I was able to build an image from an nvidia base image instead of python (as is in the Dockerfile above) that can utilize available GPUs, however the size is then much larger.
2. Is it acceptable to have a CPU-only and GPU option for the same version of a tool?
   Thank you!

[mboudet]

Hi,

I believe the issue withe GPU support is that you need to match the CUDA version in the container to the host GPU driver, so it's difficult to build in a docker (you would need to build a container for each major cuda version).

Not sure if they now manage backward / forward version support.

As for building separate version, if there are no other choices (ie, the tool built in GPU mode cannot support CPU mode), I'm not against it.

[kbestak]

From testing, the container with CUDA can still run on CPU if GPU is not provided, however since the container is then much larger, I thought it would be good to have both. I can build both and come back with the estimated container size.

[mboudet]

Ok. There is still the issue of the CUDA compatibility. I'd rather not have to build a container for each CUDA main version..

[sminot]

I would love to be able to use cellulose 3.1.0, if there is any way to merge this PR without waiting on a solution for CUDA

[kbestak]

From my side, I'd suggest setting the CUDA topic aside in that case.

[mboudet]

That's fine by me

[biocontainers-bot]

No test-cmds.txt (test file) present, skipping tests

[mboudet]

Alright, should be fine to merge. Thanks for your contribution.