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arneschneuing / DiffSBDD

A Euclidean diffusion model for structure-based drug design.
MIT License
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Problem with CoLab notebook #11

Closed drc007 closed 1 year ago

drc007 commented 1 year ago

Great work, just tried using the CoLab notebook and I get this error here.

Run sampling (this will take a few minutes; runtime depends on the input parameters n_samples, timesteps etc.)

Traceback (most recent call last): File "/content/DiffSBDD/generate_ligands.py", line 7, in from lightning_modules import LigandPocketDDPM File "/content/DiffSBDD/lightning_modules.py", line 13, in from torch_scatter import scatter_add, scatter_mean File "/usr/local/lib/python3.9/site-packages/torch_scatter/init.py", line 16, in torch.ops.load_library(spec.origin) File "/usr/local/lib/python3.9/site-packages/torch/_ops.py", line 255, in load_library ctypes.CDLL(path) File "/usr/local/lib/python3.9/ctypes/init.py", line 382, in init self._handle = _dlopen(self._name, mode) OSError: /usr/local/lib/python3.9/site-packages/torch_scatter/_version_cuda.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

arneschneuing commented 1 year ago

Hi @drc007, it seems that the environment was indeed broken. I changed the installation procedure (579513443d653a321bc2646725948ab44ef857a6) and hope that it works again. Please let me know if you encounter further issues. Thanks, Arne

drc007 commented 1 year ago

Works fine now. Thanks, Chris

evancollins1 commented 1 year ago

@arneschneuing This error still occurs for me. I am running the Colab linked in the repo exactly as it exists.

Could you help me? Thanks!