BioREx, tensorflow, and cuda toolkit

[RLWOHIO]

Does BioREx run in a Linux environment at NCBI/PubMed for PubTator3? It requires tensorflow 2.9.3, which depends on cuda toolkit 11.8. Yet, cuda toolkit 11.8 contains multiple security vulnerabilities according to our IT. I am only allowed cuda toolkit 12.6. . According to https://www.tensorflow.org/install/source_windows#gpu, tensorflow 2.11 and newer will no longer support Windows GPUs. This means BioREx/tensorflow 2.11 or later/cuda toolkit 12.x is out of question for Windows. As a result, I cannot install and run BioREx on my Windows machine.

I know my description is a bit convoluted. So could you clarify that if I can run BioREx with cuda toolkit 12.6 and an appropriate version of tensorflow on Windows? Thanks!

[ptlai]

Hi @RLWOHIO ,

Sorry for the late reply. Thank you very much for reporting this issue.

Yes, BioREx supports Linux.

If you need to run it on Cuda Toolkit 12.6 and Win11, you may need to run it on WSL2.

I updated my code to support the latest python packages requirements.txt, which might be helpful for using newer cuda toolkit version. The latest transformers deprecated some classes, so I had to update the code to support the latest packages. The current requirements.txt is for earlier transformers, and you need to replace it with this requirements.txt. There was no stable version of the cuda toolkit 12.6 package, and the only version I was able to find was 12.4 (https://pytorch.org/get-started/locally/). I have tested it on Python 3.12+Win11 WSL2+Cuda 12.4, and it works. Please let me know if you have any problems. Thanks.

[RLWOHIO]

Hi @ptlai , thanks so much for getting back and updating BioREx. I just realized that BioREx uses cuda PyTorch, NOT cuda Windows 11 toolkit (https://developer.nvidia.com/cuda-downloads?target_os=Windows&target_arch=x86_64&target_version=11&target_type=exe_local), which I am told must be version 12.6 for me to install. I will check with my IT if PyTorch with cuda 12.4 is OK with them.

Unfortunately WSL2 is off-limit to us. I do have access to run BioREx in Linux, but I figure it would be easier to debug in my local Windows machine. Thanks again!