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DirectMolecularConfGen / DMCG

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data problem #1

Closed futianfan closed 2 years ago

futianfan commented 2 years ago

hi i run the code following your instruction and got the following bugs. do you know how to fix it?

Traceback (most recent call last): File "train.py", line 359, in main() File "train.py", line 190, in main remove_hs=args.remove_hs, File "/net/sunlab/psunlab1/molecular_data/graphnn/DMCG/confgen/e2c/dataset.py", line 61, in init super().init(self.folder, transform, pre_transform) File "/nethome/tfu42/.conda/envs/dmcg2/lib/python3.7/site-packages/torch_geometric/data/in_memory_dataset.py", line 57, in init super().init(root, transform, pre_transform, pre_filter) File "/nethome/tfu42/.conda/envs/dmcg2/lib/python3.7/site-packages/torch_geometric/data/dataset.py", line 88, in init self._process() File "/nethome/tfu42/.conda/envs/dmcg2/lib/python3.7/site-packages/torch_geometric/data/dataset.py", line 171, in _process self.process() File "/net/sunlab/psunlab1/molecular_data/graphnn/DMCG/confgen/e2c/dataset.py", line 87, in process self.process_confgf() File "/net/sunlab/psunlab1/molecular_data/graphnn/DMCG/confgen/e2c/dataset.py", line 336, in process_confgf data, slices = self.collate(data_list) File "/nethome/tfu42/.conda/envs/dmcg2/lib/python3.7/site-packages/torch_geometric/data/in_memory_dataset.py", line 116, in collate add_batch=False, File "/nethome/tfu42/.conda/envs/dmcg2/lib/python3.7/site-packages/torch_geometric/data/collate.py", line 86, in collate increment) File "/nethome/tfu42/.conda/envs/dmcg2/lib/python3.7/site-packages/torch_geometric/data/collate.py", line 128, in _collate cat_dim = data_list[0].cat_dim(key, elem, stores[0]) TypeError: cat_dim() takes 3 positional arguments but 4 were given

DirectMolecularConfGen commented 2 years ago

I think this error is caused by torch_geometric version. We use torch_geometric == 1.7.2 in our code. Can you check the version you used in you conda env?

futianfan commented 2 years ago

thanks, what is your pytorch version?

futianfan commented 2 years ago

it works now. thanks!

hengck23 commented 5 months ago

the solution is found in https://github.com/pyg-team/pytorch_geometric/issues/4358

modify e2c/dataset.py


class CustomData(Data):
    def __cat_dim__(self, key, value,):

class CustomData(Data):
    def __cat_dim__(self, key, value, *args, **kwargs):