Open Yangqy-16 opened 3 months ago
Hi, I don't think this should be a dataset-specific problem. It seems that you fail to build the torch_extension
in TorchDrug. Could you check this?
Hi! Thank you for your reply! I checked my torch_extension based on https://github.com/DeepGraphLearning/torchdrug/issues/8 and https://github.com/DeepGraphLearning/torchdrug/issues/238. I'm sure that my torch_ext.cpp
lies correctly under torchdrug/utils/extension
, and I tried to delete the folder torch_extensions
which lies under /home/your_user_name/.cache
but it doesn't work.
Hello! Thank you for your great work of Torchdrug, GearNet, and ESM-GearNet! Sorry to bother you. I'm trying to extract feature embeddings using GearNet (as discussed in several former issues) on EC, GO, and FC dataset (as provided in https://zenodo.org/records/7593591). It is easy to notice that different from EC and GO where proteins are provided in pdb format, proteins in FC are in hdf5 format, so I use your Fold3d class in GearNet (https://github.com/DeepGraphLearning/GearNet/blob/main/gearnet/dataset.py) to preprocess the data. However, when I pass the Protein class into GearNet network following the instructions in Torchdrug, I met the following errors when running on GPU:
and then
When running on CPU, I met:
I searched for the cause of these errors on the Internet but found that I couldn't solve them because they are related to the environment. I'm wondering why I don't meet any of the problems when directly use Protein.from_pdb() on EC and GO, but encounter these problems on FC where I use your Fold3D class to get also data.Protein instances.
For reference, my code is as follows:
Are there any ways to solve the problem, or is my understanding of torchdrug wrong? Sincerely looking forward to your help. Thank you very much!