sokrypton / sokrypton/ColabFold
RoseTTAFold.ipynb crashes at "Install and import libraries" step in the google colab
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- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
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Description
Expected Behavior
RoseTTAFold.ipynb should install the dependencies and predict the protein structure
Current Behavior
RoseTTAFold.ipynb crashes at "Install and import libraries" step in google colab
Steps to Reproduce (for bugs)
After running the RoseTTAFold.ipynb in google colab you will see this error directly
ColabFold Output (for bugs)
Context
Possible reason is upgrade of google colab cuda driver from cuda 11 to cuda 12.
" %shell pip install -q dgl-cu113 -f https://data.dgl.ai/wheels/repo.html" This line can be the origin of the problem. Probably, need to change the dgl library and pytorch library to cuda12. Also, may need to change the rosettafold function accordingly.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with RoseTTAFold.ipynb and run the "Install and import libraries" step in Google Colab to reproduce the crash. Inspect the dgl-cu113 installation line, the PyTorch dependency, and the RoseTTAFold function in the notebook; done means the dependencies install successfully and the notebook can predict a protein structure.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python, pytorch
- Domain
- bioinformatics, cloud, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100