ONNX compatibility problems

sacdallago / biotrainer

Biological prediction models made simple.

https://biocentral.cloud/app

Academic Free License v3.0

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ONNX compatibility problems #111

Open mheinzinger opened 3 weeks ago

mheinzinger commented 3 weeks ago

Hi :) I am struggling to install bio_trainer from scratch; I proceed as described in the docs here https://github.com/sacdallago/biotrainer?tab=readme-ov-file#installation: All the packages appear to be installed correctly, except for onnxruntime; there I get the following error:

Installing onnxruntime (1.19.2): Failed

RuntimeError

Unable to find installation candidates for onnxruntime (1.19.2)

at ~/SageMaker/poetry_cache/venv/lib/python3.10/site-packages/poetry/installation/chooser.py:74 in choose_for 70│ 71│ links.append(link) 72│ 73│ if not links: → 74│ raise RuntimeError(f"Unable to find installation candidates for {package}") 75│ 76│ # Get the best link 77│ chosen = max(links, key=lambda link: self._sort_key(package, link)) 78│

Cannot install onnxruntime.

SebieF commented 3 weeks ago

Hi and thanks for asking :) Which operating system do you use (looks like some Linux system)?

Other than that, please try the following:

Is it possible to install onnxruntime via pip? pip install onnxruntime==1.19.2
Use the develop branch and see if the problem persists there (new version release is coming up soon anyway)

mheinzinger commented 1 week ago

I am on Amazon Linux release 2 (Karoo) - (using SageMaker). The python version I am using is 3.10.12. I had also already tried installing onnxruntime via pip as you stated above but there I am running into the same issue: pip install onnxruntime==1.19.2 ERROR: Could not find a version that satisfies the requirement onnxruntime==1.19.2 (from versions: 1.12.0, 1.12.1, 1.13.1, 1.14.0, 1.14.1, 1.15.0, 1.15.1, 1.16.0, 1.16.1, 1.16.2, 1.16.3) ERROR: No matching distribution found for onnxruntime==1.19.2 Installing from develop branch also lead to the same error

SebieF commented 1 week ago

Please try again with the main branch, because the latest version release should use onnxruntime==1.19.0. See the latest commit to the dependencies: https://github.com/sacdallago/biotrainer/commit/8e5dd655ba3a10f57afb70ae0afac356fbb3369f#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R55

SebieF commented 12 hours ago

The problem is not fixed yet on all machines, please also refer to this issue if you are experiencing problems (especially with Windows) currently: https://github.com/onnx/onnx/issues/6267