Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

CUDA index out of bounds #4

Open
BL-Lac149597870 opened this issue Nov 18, 2023 · 4 comments
Open

CUDA index out of bounds #4

BL-Lac149597870 opened this issue Nov 18, 2023 · 4 comments

Comments

@BL-Lac149597870
Copy link

When I executed the 'inference.py' script, I encountered a CUDA error. The error message is displayed in the following image:

image

This error occurred immediately after the script completed executing line 121 and began processing line 24. Any ideas for this bug?

@zytzrh
Copy link
Collaborator

zytzrh commented Dec 24, 2023

Hi @BL-Lac149597870, this error seems to indicate the it is attempting to access an element of a tensor or array at an index that does not exist. Have you checked the the maximum value of protein.atom2graph and the shape of sigma?

@BL-Lac149597870
Copy link
Author

The error occured before the script executing line 124. It appears there may be an issue with the graph_construction_model. Removing the SpatialEdge and KNNEdge classes from the train.yaml file resolves the previously mentioned error.
image

@zytzrh
Copy link
Collaborator

zytzrh commented Dec 28, 2023

Hi @BL-Lac149597870, can you locate which pdb cause this issue and share the file?

@BL-Lac149597870
Copy link
Author

Hi @zytzrh ,I've reviewed the source code of TorchDrug and noticed an issue related to the computation of the explicit_valence property. This can be found in the TorchDrug repository here: https://github.com/DeepGraphLearning/torchdrug/blob/6066fbd82360abb5f270cba1eca560af01b8cc90/torchdrug/data/molecule.py#L511C5-L514C47. It's important to note that this doesn't affect the operation of DiffPack. Regarding the graph construction in DiffPack, observed here:https://github.com/DeepGraphLearning/DiffPack/blob/81ee51612abfab5af23a8d33fbb081a024f83a1c/diffpack/task.py#L116C1-L121C61 , it appears that additional edge types are incorporated into the edge_list . However, bond2valence lacks corresponding values for these new edge types.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants