google-deepmind / google-deepmind/alphafold
Alphafold stopped using GPU after upgrade to Ubuntu 24.04.1 (noble)
- Dominant language
- Python
- Stars
- 14.9k
- Forks
- 2.9k
- PR merge metrics
- No merged PRs in 30d
Description
I have been runing the current version of Alphafold successfully on a linux machine with Ubuntu 22.04 and an Nvidia 4090 GPU. After some automatic update (graphics driver, maybe?) , it mysteriously was getting super slow, probably in CPU mode. I decided to upgrade the machin to 24.04.1 (noble), which was probably a bad idea. It made matters worse, in the end I installed everything new:
Nvidia graphics driver 560.35.03 (open)
Docker 27.3.1
Nvidia container toolkit 1.16.2-1
and the usual stuff that goes with Ubuntu 24.04.1 (python 3.12.3, gcc 13.2.0)
I followed the instruction, as I did in the previous successful installations. First problem was with the Dockerfile, covered in https://github.com/google-deepmind/alphafold/issues/945 I 'fixed' it by following the comments of "rosswalker" which also worked for others. This allowed me to build the docker image. The databases were still installed, I just edited run_docker.py for setting the database and output paths.
However, the big problem: When running alphafold, I got the following error message:
I1024 21:50:40.124427 127699774173312 run_docker.py:260] I1024 19:50:40.123955 136147855569536 xla_bridge.py:863] Unable to initialize backend 'cuda': jaxlib/cuda/versions_helpers.cc:98: operation cuInit(0) failed: Unknown CUDA error 303; cuGetErrorName failed. This probably means that JAX was unable to load the CUDA libraries.
I know nothing about DOCKER and really don't know what I am doing. This message looks like CUDA is not found (?). Before that line, there was another suspicious output, but I am not sure if it is related:
I1024 21:50:38.367850 127699774173312 run_docker.py:260] /bin/bash: /opt/conda/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Maybe someone has solved this problem or can share a Dockerfile that works on Ubuntu 24.4.01 with a contemporary (4XXX) Nvidia GPU? Or maybe I should use another version of Docker or CUDA?
Contributor guide
Assessment
This issue has not been assessed yet.