demos

[xiaorandu]

Following up on my previous post, I tried to run all the demos, however, for each of them I failed at its last step, and received the pretty much the similar error.
`
TypeError Traceback (most recent call last)
in <cell line: 9>()
8
9 for epoch in range(1, args.epochs + 1):
---> 10 loss_acc = train_func(model, device, train_loader, optimizer)
11 print("Epoch: {}\nLoss: {}".format(epoch, loss_acc))
12

5 frames
/usr/local/lib/python3.10/dist-packages/torch/_utils.py in reraise(self)
720 # instantiate since we don't know how to
721 raise RuntimeError(msg) from None
--> 722 raise exception
723
724

TypeError: Caught TypeError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/usr/local/lib/python3.10/dist-packages/torch/utils/data/_utils/worker.py", line 308, in _worker_loop
data = fetcher.fetch(index)
File "/usr/local/lib/python3.10/dist-packages/torch/utils/data/_utils/fetch.py", line 51, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/usr/local/lib/python3.10/dist-packages/torch/utils/data/_utils/fetch.py", line 51, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/usr/local/lib/python3.10/dist-packages/torch_geometric/data/dataset.py", line 289, in getitem
data = self.get(self.indices()[idx])
File "/content/drive/MyDrive/MoleculeSTM/MoleculeSTM/datasets/MoleculeNet_Graph.py", line 184, in get
for key in self.data.keys:
TypeError: 'method' object is not iterable
`
Could you provide some insights on how to address this issue? Thank you!

[xiaorandu]

btw, I run the demo code in google colab (Python 3.10), and here are the installed packages, not sure if it is the compatible issue.
`
!pip install rdkit
!pip install torch torchvision
!pip install requests tqdm matplotlib spacy Levenshtein boto3 deepspeed
!pip install ogb==1.2.0
!pip install transformers==4.30.2

!pip install torch_geometric
!pip install torch-scatter -f https://data.pyg.org/whl/torch-2.2.1+cu121.html
!pip install torch-sparse -f https://data.pyg.org/whl/torch-2.2.1+cu121.html
!pip install torch-cluster -f https://data.pyg.org/whl/torch-2.2.1+cu121.html
!pip install torch-spline-conv -f https://data.pyg.org/whl/torch-2.2.1+cu121.html
!pip install git+https://github.com/MolecularAI/pysmilesutils.git

!git clone https://github.com/chao1224/apex.git
%cd apex
!pip install -v --disable-pip-version-check --no-cache-dir ./
%cd ..
`