Pytorch downgrades to a lower version

[thepowerfuldeez]

Hi! Is there functionality to ignore dependencies if they are already exist in the system python?
I am using nvcr.io/nvidia/pytorch:24.08-py3 docker image which has pytorch==2.5.0a0+872d972e41.nv24.08 installed

I followed guide from here to enable system python via UV_SYSTEM_PYTHON=1 and I have pyproject.toml that includes packages that I've put from requirements.txt and made uv lock.

But now I see that it's been resolved with torch==2.4.0 and when I run uv sync my pytorch gets downgraded to 2.4.0 which is unexpected.
I have tried to manually remove all pytorch dependencies from lockfile and run uv sync from that state, but for some reason now it suceeds with installing only 4 of 126 packages (and they are just file packages from file://... defined in pyproject.toml)
I've tried using uv sync --frozen uv sync --locked and tried creating uv sync with different variations but haven't suceeded yet. To be frank pip install -r requirements.txt would also downgrade my torch unless I make pip freeze > requirements.txt and install with -r --no-deps but this is not favorable.

I generally lack understanding of such intricacies and I've noticed that other people stumble with flash-attn installation or CUDA extensions. I wonder what's the best way to handle such conflicts?
Thank you very much for modern replacement of pip!

[thepowerfuldeez]

Example of downgrading torch (and installing cuda extensions which are not needed)

> uv sync
Resolved 127 packages in 567ms
⠧ Preparing packages... (5/13)
nvidia-cufft-cu12 ------------------------------ 58.53 MB/121.64 MB
nvidia-cusolver-cu12 ------------------------------ 58.41 MB/124.16 MB
nvidia-nccl-cu12 ------------------------------ 58.49 MB/176.25 MB
nvidia-cusparse-cu12 ------------------------------ 58.55 MB/195.96 MB
nvidia-cublas-cu12 ------------------------------ 58.29 MB/410.59 MB
nvidia-cudnn-cu12 ------------------------------ 58.35 MB/664.75 MB
torch      ------------------------------ 33.03 MB/797.23 MB
^C```

[charliermarsh]

This doesn't work today with uv sync or uv lock -- it won't respect existing environments. The lower-level uv pip APIs do, though. You can run uv pip install with an active virtual environment, and it will retain existing versions of PyTorch, if they're already installed.

[thepowerfuldeez]

@charliermarsh how do I respect pyproject.toml and use project setup features? I thought of switching to uv as a project management tool (similar to poetry or rye if that matter). Will uv pip install -r pyproject.toml work?
What's the proposed approach for project management for ML workflows? This is highly requested imo, would glad to have clear guide :)

[charliermarsh]

Yeah uv pip install -r pyproject.toml should work just fine. In general, our goal is for folks to use the "higher-level" project APIs (uv lock, uv sync, etc.). But in this case, if you're using an nvidia image that has packages pre-installed, it won't play correctly with uv lock and uv sync. So if you want to build atop that base environment, you'll need to use the "lower-level" uv pip APIs.

E.g., activate that virtual environment, then run uv pip install -r pyproject.toml.

[thepowerfuldeez]

@charliermarsh This doesn't work
I have tried

> uv venv --python-preference only-system --system-site-packages
source .venv/bin/activate
uv pip install -r pyproject.toml

It still installs torch==2.4.0 even though it's not in the dependencies of pyproject.toml

I verified that inside this venv torch is installed

[thepowerfuldeez]

@charliermarsh I have tried to set

[tool.uv]
# Always install torch 2.5, regardless of whether transitive dependencies request
# a different version.
override-dependencies = ["torch==2.5.0a0+872d972e41.nv24.08"]

but it can't be resolved

× No solution found when resolving dependencies:
  ╰─▶ Because there is no version of torch==2.5.0a0+872d972e41.nv24.8 and accelerate==0.33.0 depends on torch==2.5.0a0+872d972e41.nv24.8, we can conclude that accelerate==0.33.0 cannot be used.

[charliermarsh]

@thepowerfuldeez -- If you're trying to use packages from the system Python, you'll need to use uv pip install --system -r pyproject.toml, and avoid creating a virtual environment at all. Can you try that?

[thepowerfuldeez]

@charliermarsh Thank you so much! It works now! So the solution is not using lockfile for now, right?

[charliermarsh]

Unfortunately yes. We'll need to think on how to solve this properly.

[charliermarsh]

I'm gonna leave the issue open but might tweak the title and add some more details on the underlying problem, if that's ok.

[awoimbee]

I had the same issue with poetry some time ago: python-poetry/poetry#6035 (resolved by python-poetry/poetry#8359).

Note uv venv --system-site-packages exists since #2101, but "we won't take the system site packages into account in subsequent commands".

[zanieb]

@charliermarsh it seems like there might be a real issue to track here?

[charliermarsh]

Yeah. The system packages aren't taken into account.