Alex Holehouse

Thanks for the quick response! So I'd actually done exactly this (albeit backwards - install mdtraj with dependencies, then uninstall ONLY mdtraj with `--force` flag, and reinstall again). This, and...

@rmcgibbo - absolutely; well aware, and your involvement here has been above and beyond anyone's wildest dreams :). Actually, providing a greater level of administrative/computational support for mdtraj is something...

YES! At least the original issue I had now works! Thanks all; please feel free to close this!

To chime in here (because I think I have the same issue), maybe I've misunderstood, but the Dockerfile in `alphafold/docker/` requests a CUDA 11.1.1 version, and the CUDA version on...

> > > I want to know if this error could influence the outcome of the prediction or just let the jackhmmer step to be slow > > > >...

See issue [https://github.com/google-deepmind/alphafold/issues/812](https://github.com/google-deepmind/alphafold/issues/812) which may offer a resolution that works for you

I believe this is because [the image was removed, as per this comment](https://github.com/NVIDIA/nvidia-docker/issues/1735#issuecomment-1455744048). On Ubuntu 20.04 the following should work: `docker run --rm --gpus all nvidia/cuda:11.0.3-base-ubuntu20.04 nvidia-smi`

Exactly the same issue here; same errors and while it runs things are breathtakingly slow. My `nvidia-smi` output - `pid 272923` is the `python /app/alphafold/run_alphafold.py` proc. ``` +-----------------------------------------------------------------------------+ | NVIDIA-SMI...