TypeError: __inc__() takes 3 positional arguments but 4 were given +torch_geometric/data/collate.py

[WGDMS]

😵 Describe the installation problem

Dear Team: I received the following error. Hope that it is a version problem.

---> 19 run_classification(train_dataset, val_dataset, test_dataset, model, num_tasks, epochs, batch_size, vt_batch_size, lr, lr_decay_factor, lr_decay_step_size, weight_decay, early_stopping, loss, metric, log_dir, save_dir,True)

10 frames /usr/local/lib/python3.7/dist-packages/torch_geometric/data/collate.py in (.0) 223 repeats = [ 224 data.inc(key, value, store) --> 225 for value, data, store in zip(values, data_list, stores) 226 ] 227 if isinstance(repeats[0], Tensor):

TypeError: inc() takes 3 positional arguments but 4 were given

Please help me to solve this.

Environment

• PyG version: 2.0.4
• PyTorch version:1.10.0
• OS: Windows
• Python version: 3.7.13
• CUDA/cuDNN version:11.1
• How you installed PyTorch and PyG (conda, pip, source): !pip install torch torch-scatter torch-sparse torch-cluster torch-spline-conv torchaudio torch-geometric -f https://data.pyg.org/whl/torch-1.10.0+cu111.html
• Any other relevant information (e.g., version of torch-scatter):

[rusty1s]

Which could do you try to run? With PyG>=2.0, there was a change in the expected input arguments of data.__inc__ and data.cat_dim` (which now expect four arguments rather than three). This is documented here. You can easily fix this by adjusting the function headers to:

def __cat_dim__(self, key, value, *args, **kwargs):
    pass
  
def __inc__(self, key, value, *args, **kwargs):
    pass

[Abbas009]

I am using pyg>=2.0.5 torch =1.10.0 Python = 3.7.11 OS: Linux And I am still getting this error. Pair data is what data contains and i have created sub_g as subgraph from whole graph. PairData(x=[200, 52], y=[1], pos=[200, 2], sub_g=[16, 50, 52], edge_index=[2, 1335], patch_idx=[1]) PairData(x=[296, 52], y=[1], pos=[296, 2], sub_g=[16, 50, 52], edge_index=[2, 2138], patch_idx=[1]) PairData(x=[279, 52], y=[1], pos=[279, 2], sub_g=[16, 50, 52], edge_index=[2, 2021], patch_idx=[1]) Traceback (most recent call last): File "train.py", line 491, in main() File "train.py", line 483, in main cell_graph(prog_args, writer=writer) File "train.py", line 364, in cell_graph writer=writer) File "train.py", line 243, in train for idx, data in enumerate(dataset): File "/compuworks/anaconda3/envs/tandoan2/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 521, in next data = self._next_data() File "/compuworks/anaconda3/envs/tandoan2/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 561, in _next_data data = self._dataset_fetcher.fetch(index) # may raise StopIteration File "/compuworks/anaconda3/envs/tandoan2/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 52, in fetch return self.collate_fn(data) File "/compuworks/anaconda3/envs/tandoan2/lib/python3.7/site-packages/torch_geometric/loader/dataloader.py", line 20, in call self.exclude_keys) File "/compuworks/anaconda3/envs/tandoan2/lib/python3.7/site-packages/torch_geometric/data/batch.py", line 74, in from_data_list exclude_keys=exclude_keys, File "/compuworks/anaconda3/envs/tandoan2/lib/python3.7/site-packages/torch_geometric/data/collate.py", line 85, in collate increment) File "/compuworks/anaconda3/envs/tandoan2/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

I have checked def cat_dim and def inc as similar in the newer version as you have described above but still getting this error. Any solution?

[rusty1s]

Did you apply the above suggestion?

def __cat_dim__(self, key, value, *args, **kwargs):
    pass
  
def __inc__(self, key, value, *args, **kwargs):
    pass

[Abbas009]

Yes, In the newer version it already as it is mentioned by you. What other reason could be for this error, is this related to the version or related to the dataset?

[rusty1s]

I'm not sure which code you are running. But if you changed it as it is mentioned above, you may need to ensure to re-install the package such that the modifications are taken into account.

[yuxinl915]

I'm not sure which code you are running. But if you changed it as it is mentioned above, you may need to ensure to re-install the package such that the modifications are taken into account.

Hi! Thanks so much for your help! But could please provide more details on how to re-install the package?

[rusty1s]

Do you see the same error? Does adjusting the __cat_dim__ and __inc__ properties as mentioned here not help? You can re-install the package via

pip install --upgrade torch-geometric

[yuxinl915]

Do you see the same error? Does adjusting the __cat_dim__ and __inc__ properties as mentioned here not help? You can re-install the package via

pip install --upgrade torch-geometric

Thanks so much for your reply! But if do so, new problems occur shown as below. This problem is not accidental that I encountered it every time I did the operation you mentioned when dealing with several different projects. Could you please give me some tips about that? Really appreciate it!

env/lib/python3.8/site-packages/torch_geometric/data/separate.py", line 65, in _separate value = value.narrow(cat_dim or 0, start, end - start) IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 43204744)

[rusty1s]

Is it possible for you to share some of the data objects with a small reproducible script? I am sure the error is easy to solve.

[yuxinl915]

@rusty1s Thanks so much for your reply! Could you please provide me with an email, so that I can share some files?

[rusty1s]

At best, you can share the link here so others can chime in as well. Alternatively, you can find my mail on my github profile.

[yuxinl915]

data.txt This is my current data.py file from env/lib/python3.8/site-packages/torch_geometric/data/data.py. I modified the original code from lines 502 - 516.

[rusty1s]

Oh, it looks like there is some mis-understanding. You do not need to modify the PyG source code (which will in fact result in breaking PyG) - instead, there seems to exist a data object in your code that inherits from torch_geometric.data.Data and which re-implements the __cat_dim__ and __inc__ interface. Simply changing these functions to the new function headers

def __cat_dim__(self, key, value, *args, **kwargs):
def __inc__(self, key, value, *args, **kwargs):

should resolve this.

[yuxinl915]

Cool! I will try it out! Thanks so much!!!

On Wed, Sep 7, 2022 at 1:48 AM Matthias Fey @.***> wrote:

Oh, it looks like there is some mis-understanding. You do not need to modify the PyG source code (and will in fact result in breaking PyG) - instead, there seems to be a data object in your code that inherits from torch_geometric.data.Data and which re-implements the cat_dim and inc interface. Simply changing these functions to the new function headers

def cat_dim(self, key, value, *args, **kwargs):def inc(self, key, value, *args, **kwargs):

should resolve this.

— Reply to this email directly, view it on GitHub https://github.com/pyg-team/pytorch_geometric/issues/4358#issuecomment-1238934670, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARSRTYYBIR3BIMDDR6FT3JDV5AUEBANCNFSM5RYUEXWQ . You are receiving this because you commented.Message ID: @.***>

[sirlddf]

In PyG version 2.3, the solution mentioned before doesn't work. However, I solve the problem by arrange the input of the function inc in the collate.py file.

The relative of the function I modified is as follows: anaconda3/envs/${your env name}/lib/python3.9/site-pacakages/torch_geometric/data/collate.py/get_incs

def get_incs(key, values: List[Any], data_list: List[BaseData]), stores: List[BaseStorage]) -> Tensor: """ ### original version which will cause TypeError... repeats = [ data.inc(key, value, store) for value, data, store in zip(values, data_list, stores) ] """ ### modified version, while may cause other problems we do not expect currently repeats = [ data.inc(key, value) for value, data, store in zip(values, data_list, stores) ] ... return cumsum(repeats[:-1])

my environment details: python=3.9 torch=1.13.1 + cu116 torch-geometric=2.3

Hope this can help you

[zaplm]

Thank you @sirlddf, this problem has been bothering me for a long time, and I finally managed to solve it by using your method.

[Jctrp]

In PyG version 2.3, the solution mentioned before doesn't work. However, I solve the problem by arrange the input of the function inc in the collate.py file.

The relative of the function I modified is as follows: anaconda3/envs/${your env name}/lib/python3.9/site-pacakages/torch_geometric/data/collate.py/get_incs

def get_incs(key, values: List[Any], data_list: List[BaseData]), stores: List[BaseStorage]) -> Tensor: """ ### original version which will cause TypeError... repeats = [ data.inc(key, value, store) for value, data, store in zip(values, data_list, stores) ] """ ### modified version, while may cause other problems we do not expect currently repeats = [ data.inc(key, value) for value, data, store in zip(values, data_list, stores) ] ... return cumsum(repeats[:-1])

my environment details: python=3.9 torch=1.13.1 + cu116 torch-geometric=2.3

Hope this can help you

It works, thank you.

[rankupup]

In PyG version 2.3, the solution mentioned before doesn't work. However, I solve the problem by arrange the input of the function inc in the collate.py file.

The relative of the function I modified is as follows: anaconda3/envs/${your env name}/lib/python3.9/site-pacakages/torch_geometric/data/collate.py/get_incs

def get_incs(key, values: List[Any], data_list: List[BaseData]), stores: List[BaseStorage]) -> Tensor: """ ### original version which will cause TypeError... repeats = [ data.inc(key, value, store) for value, data, store in zip(values, data_list, stores) ] """ ### modified version, while may cause other problems we do not expect currently repeats = [ data.inc(key, value) for value, data, store in zip(values, data_list, stores) ] ... return cumsum(repeats[:-1])

my environment details: python=3.9 torch=1.13.1 + cu116 torch-geometric=2.3

Hope this can help you

It works!!!Thank you very much!!