RuntimeError: incompatible bytecode version when loading UMAP model from pickle

[JaVanGri]

I encountered a RuntimeError while attempting to load a pre-trained UMAP model from a pickle file and apply a transformation to an array. The error message indicates an incompatible bytecode version. I am using Python 3.8 and the dependencies from the requirements.txt file. I encountered this issue on both Windows and Linux.

Error message:

[f-kretschmer]

Hi, could you check your numba-version specifically? I know there are problems with versions different to 0.53.1. SciPy, umap-learn and numba have to have the exact versions specified in the requirements.txt. Are you using pip or mamba/conda for the packages?

[JaVanGri]

Hi, thanks for the suggestion! I checked my package versions, and they match exactly:

• umap-learn: 0.5.3
• numba: 0.53.1
• scipy: 1.7.1

I set up two different Python environments. In one, I installed the requirements using pip, and in the other, I used conda. Both encountered the same issue.

Could it be possible that the file umap_embedding_biostructures.pkl from https://osf.io/5sxfe/ is broken? I’m not sure if the error stem from the file itself rather than the environment.

[f-kretschmer]

I checked the file on OSF, and it should be the correct one (m5dsum: 661cc8ff2cd918894e15729180554ff8). I also re-checked that it works in my environment. I'll try to make a cloudpickle version of the file, but I'm out of the office right now, so I'm sorry, might take a bit.

[f-kretschmer]

Here is a link to the cloudpickle version, maybe that works: https://upload.uni-jena.de/data/66ea7c206f1044.70440131/umap_embedding_biostructures_cp.pkl As I understand it, the python version has to be the same (3.9.18 for me), but otherwise dependency versions don't matter for cloudpickle. The cloudpickle version is 3.0.0. By the way, have you checked the MD5 checksum for the pickle file?

[JaVanGri]

Thanks again for your prompt help! The MD5 cheksum was correct. Using Python 3.9.18 solved the issue. I would suggest adding a note in the README.md to specify the required Python version for future users.

[f-kretschmer]

Thanks, glad that it finally worked. I will add that to the README.