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divelab / GOOD

GOOD: A Graph Out-of-Distribution Benchmark [NeurIPS 2022 Datasets and Benchmarks]
https://good.readthedocs.io/
GNU General Public License v3.0
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run CIGA algorithm error #13

Closed czstudio closed 1 year ago

czstudio commented 1 year ago

when i run !goodtg --config_path GOOD_configs/GOODCMNIST/color/concept/CIGA.yaml in colab:


2023-05-07` 13:42:38.808831: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-05-07 13:42:40.848157: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
This logger will substitute general print function

INFO: -----------------------------------
    Task: train
Sun May  7 13:42:43 2023
INFO: Load Dataset GOODCMNIST
Downloading...
From: https://drive.google.com/uc?id=1F2r2kVmA0X07AXyap9Y_rOM6LipDzwhq
To: /content/GOOD/storage/datasets/GOODCMNIST.zip
100%|##########| 719M/719M [00:03<00:00, 225MB/s]
Extracting /content/GOOD/storage/datasets/GOODCMNIST.zip
DEBUG: 05/07/2023 01:43:41 PM : Dataset: {'train': GOODCMNIST(29400), 'id_val': GOODCMNIST(6300), 'id_test': GOODCMNIST(6300), 'val': GOODCMNIST(14000), 'test': GOODCMNIST(14000), 'task': 'Multi-label classification', 'metric': 'Accuracy'}
DEBUG: 05/07/2023 01:43:41 PM :  Data(x=[75, 3], edge_index=[2, 1367], y=[1], pos=[75, 2], color=[1], env_id=[1])
INFO: Loading model...
DEBUG: 05/07/2023 01:43:41 PM : Config model
DEBUG: 05/07/2023 01:43:45 PM : Load training utils
INFO: Epoch 0:
/usr/local/lib/python3.10/dist-packages/torch_geometric/data/in_memory_dataset.py:182: UserWarning: It is not recommended to directly access the internal storage format `data` of an 'InMemoryDataset'. The data of the dataset is already cached, so any modifications to `data` will not be reflected when accessing its elements. Clearing the cache now by removing all elements in `dataset._data_list`. If you are absolutely certain what you are doing, access the internal storage via `InMemoryDataset._data` instead to suppress this warning. Alternatively, you can access stacked individual attributes of every graph via `dataset.{attr_name}`.
  warnings.warn(msg)
/usr/local/lib/python3.10/dist-packages/torch_geometric/data/in_memory_dataset.py:182: UserWarning: It is not recommended to directly access the internal storage format `data` of an 'InMemoryDataset'. If you are absolutely certain what you are doing, access the internal storage via `InMemoryDataset._data` instead to suppress this warning. Alternatively, you can access stacked individual attributes of every graph via `dataset.{attr_name}`.
  warnings.warn(msg)
  0%|░░░░░░░░░░░░░░░░░░░░| 0/230 [00:01<?, ?it/s]
ERROR: 05/07/2023 01:43:47 PM - utils.py - line 87 : Traceback (most recent call last):
  File "/usr/local/bin/goodtg", line 33, in <module>
    sys.exit(load_entry_point('graph-ood', 'console_scripts', 'goodtg')())
  File "/content/GOOD/GOOD/kernel/main.py", line 69, in goodtg
    main()
  File "/content/GOOD/GOOD/kernel/main.py", line 60, in main
    pipeline.load_task()
  File "/content/GOOD/GOOD/kernel/pipelines/basic_pipeline.py", line 231, in load_task
    self.train()
  File "/content/GOOD/GOOD/kernel/pipelines/basic_pipeline.py", line 113, in train
    train_stat = self.train_batch(data, pbar)
  File "/content/GOOD/GOOD/kernel/pipelines/basic_pipeline.py", line 71, in train_batch
    model_output = self.model(data=data, edge_weight=edge_weight, ood_algorithm=self.ood_algorithm)
  File "/usr/local/lib/python3.10/dist-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/content/GOOD/GOOD/networks/models/CIGAGNN.py", line 73, in forward
    causal_rep = self.get_graph_rep(
  File "/content/GOOD/GOOD/networks/models/CIGAGNN.py", line 108, in get_graph_rep
    return self.feat_encoder(*args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/content/GOOD/GOOD/networks/models/GINs.py", line 94, in forward
    out_readout = self.encoder(x, edge_index, batch, batch_size, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/content/GOOD/GOOD/networks/models/GINvirtualnode.py", line 118, in forward
    post_conv = self.dropout1(self.relu1(self.batch_norm1(self.conv1(x, edge_index))))
  File "/usr/local/lib/python3.10/dist-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/torch_geometric/nn/conv/gin_conv.py", line 80, in forward
    out = self.propagate(edge_index, x=x, size=size)
  File "/usr/local/lib/python3.10/dist-packages/torch_geometric/nn/conv/message_passing.py", line 476, in propagate
    explain_msg_kwargs = self.inspector.distribute(
  File "/usr/local/lib/python3.10/dist-packages/torch_geometric/nn/conv/utils/inspector.py", line 54, in distribute
    for key, param in self.params[func_name].items():
KeyError: 'explain_message'
CM-BF commented 1 year ago

Hi @czstudio,

Thank you for your post. But I couldn't reproduce your error, and I found no clue why there is an 'explain_message' key. Can you share your package list? :)

Best, Shurui

czstudio commented 1 year ago

Thank you for your reply!!! my pip list are : Package Version Editable project location

absl-py 1.4.0 alabaster 0.7.13 albumentations 1.2.1 altair 4.2.2 antlr4-python3-runtime 4.9.3 anyio 3.6.2 appdirs 1.4.4 argon2-cffi 21.3.0 argon2-cffi-bindings 21.2.0 arviz 0.15.1 astropy 5.2.2 astunparse 1.6.3 attrs 23.1.0 audioread 3.0.0 autograd 1.5 Babel 2.12.1 backcall 0.2.0 beautifulsoup4 4.11.2 bleach 6.0.0 blis 0.7.9 blosc2 2.0.0 bokeh 2.4.3 branca 0.6.0 CacheControl 0.12.11 cached-property 1.5.2 cachetools 5.3.0 captum 0.2.0 catalogue 2.0.8 certifi 2022.12.7 cffi 1.15.1 chardet 4.0.0 charset-normalizer 2.0.12 chex 0.1.7 cilog 1.3.0 click 8.1.3 cloudpickle 2.2.1 cmake 3.25.2 cmdstanpy 1.1.0 colorcet 3.0.1 colorlover 0.3.0 community 1.0.0b1 confection 0.0.4 cons 0.4.5 contextlib2 0.6.0.post1 contourpy 1.0.7 convertdate 2.4.0 coverage 7.2.5 cryptography 40.0.2 cufflinks 0.17.3 cvxopt 1.3.0 cvxpy 1.3.1 cycler 0.11.0 cymem 2.0.7 Cython 0.29.34 dask 2022.12.1 datascience 0.17.6 db-dtypes 1.1.1 dbus-python 1.2.16 debugpy 1.6.6 decorator 4.4.2 defusedxml 0.7.1 distributed 2022.12.1 dive-into-graphs 1.1.0 dlib 19.24.1 dm-tree 0.1.8 docutils 0.16 dopamine-rl 4.0.6 duckdb 0.7.1 earthengine-api 0.1.350 easydict 1.10 ecos 2.0.12 editdistance 0.6.2 en-core-web-sm 3.5.0 entrypoints 0.4 ephem 4.1.4 et-xmlfile 1.1.0 etils 1.2.0 etuples 0.3.8 exceptiongroup 1.1.1 execnet 1.9.0 fastai 2.7.12 fastcore 1.5.29 fastdownload 0.0.7 fastjsonschema 2.16.3 fastprogress 1.0.3 fastrlock 0.8.1 filelock 3.12.0 firebase-admin 5.3.0 Flask 2.2.4 flatbuffers 23.3.3 flax 0.6.9 folium 0.14.0 fonttools 4.39.3 frozendict 2.3.7 fsspec 2023.4.0 future 0.18.3 gast 0.4.0 GDAL 3.3.2 gdown 4.6.6 gensim 4.3.1 geographiclib 2.0 geopy 2.3.0 gin-config 0.5.0 glob2 0.7 google 2.0.3 google-api-core 2.11.0 google-api-python-client 2.84.0 google-auth 2.17.3 google-auth-httplib2 0.1.0 google-auth-oauthlib 0.4.6 google-cloud-bigquery 3.9.0 google-cloud-bigquery-storage 2.19.1 google-cloud-core 2.3.2 google-cloud-datastore 2.15.1 google-cloud-firestore 2.11.0 google-cloud-language 2.9.1 google-cloud-storage 2.8.0 google-cloud-translate 3.11.1 google-colab 1.0.0 google-crc32c 1.5.0 google-pasta 0.2.0 google-resumable-media 2.5.0 googleapis-common-protos 1.59.0 googledrivedownloader 0.4 graph-ood 1.1.1 /content/GOOD graphviz 0.20.1 greenlet 2.0.2 grpcio 1.54.0 grpcio-status 1.48.2 gspread 3.4.2 gspread-dataframe 3.0.8 gym 0.25.2 gym-notices 0.0.8 h5netcdf 1.1.0 h5py 3.8.0 hijri-converter 2.3.1 holidays 0.23 holoviews 1.15.4 html5lib 1.1 httpimport 1.3.0 httplib2 0.21.0 humanize 4.6.0 hydra-core 1.3.2 hyperopt 0.2.7 idna 3.4 imageio 2.25.1 imageio-ffmpeg 0.4.8 imagesize 1.4.1 imbalanced-learn 0.10.1 imgaug 0.4.0 importlib-resources 5.12.0 imutils 0.5.4 inflect 6.0.4 iniconfig 2.0.0 intel-openmp 2023.1.0 ipykernel 5.5.6 ipython 7.34.0 ipython-genutils 0.2.0 ipython-sql 0.4.1 ipywidgets 7.7.1 itsdangerous 2.1.2 jax 0.4.8 jaxlib 0.4.7+cuda11.cudnn86 jedi 0.18.2 jieba 0.42.1 Jinja2 3.1.2 joblib 1.2.0 jsonpickle 3.0.1 jsonschema 4.3.3 jupyter-client 6.1.12 jupyter-console 6.1.0 jupyter_core 5.3.0 jupyter-server 1.24.0 jupyterlab-pygments 0.2.2 jupyterlab-widgets 3.0.7 kaggle 1.5.13 keras 2.12.0 kiwisolver 1.4.4 korean-lunar-calendar 0.3.1 langcodes 3.3.0 lazy_loader 0.2 libclang 16.0.0 librosa 0.10.0.post2 lightgbm 3.3.5 lit 16.0.2 littleutils 0.2.2 llvmlite 0.39.1 locket 1.0.0 logical-unification 0.4.5 LunarCalendar 0.0.9 lxml 4.9.2 Markdown 3.4.3 markdown-it-py 2.2.0 MarkupSafe 2.1.2 matplotlib 3.5.2 matplotlib-inline 0.1.6 matplotlib-venn 0.11.9 mdurl 0.1.2 miniKanren 1.0.3 missingno 0.5.2 mistune 0.8.4 mizani 0.8.1 mkl 2019.0 ml-dtypes 0.1.0 mlxtend 0.14.0 more-itertools 9.1.0 moviepy 1.0.3 mpmath 1.3.0 msgpack 1.0.5 multipledispatch 0.6.0 multitasking 0.0.11 munch 2.5.0 murmurhash 1.0.9 music21 8.1.0 mypy-extensions 1.0.0 natsort 8.3.1 nbclient 0.7.4 nbconvert 6.5.4 nbformat 5.8.0 nest-asyncio 1.5.6 networkx 2.8 nibabel 3.0.2 nltk 3.8.1 notebook 6.4.8 numba 0.56.4 numexpr 2.8.4 numpy 1.22.4 oauth2client 4.1.3 oauthlib 3.2.2 ogb 1.3.6 omegaconf 2.3.0 opencv-contrib-python 4.7.0.72 opencv-python 4.7.0.72 opencv-python-headless 4.7.0.72 openpyxl 3.0.10 opt-einsum 3.3.0 optax 0.1.5 orbax-checkpoint 0.2.1 osqp 0.6.2.post8 outdated 0.2.2 packaging 23.1 palettable 3.3.3 pandas 1.5.3 pandas-datareader 0.10.0 pandas-gbq 0.17.9 pandocfilters 1.5.0 panel 0.14.4 param 1.13.0 parso 0.8.3 partd 1.4.0 pathlib 1.0.1 pathy 0.10.1 patsy 0.5.3 pep517 0.13.0 pexpect 4.8.0 pickleshare 0.7.5 Pillow 8.4.0 pip 23.0.1 pip-tools 6.6.2 platformdirs 3.3.0 plotly 5.13.1 plotnine 0.10.1 pluggy 1.0.0 polars 0.17.3 pooch 1.6.0 portpicker 1.3.9 prefetch-generator 1.0.3 preshed 3.0.8 prettytable 0.7.2 proglog 0.1.10 progressbar2 4.2.0 prometheus-client 0.16.0 promise 2.3 prompt-toolkit 3.0.38 prophet 1.1.2 proto-plus 1.22.2 protobuf 3.20.1 psutil 5.9.5 psycopg2 2.9.6 ptyprocess 0.7.0 py 1.11.0 py-cpuinfo 9.0.0 py4j 0.10.9.7 pyarrow 9.0.0 pyasn1 0.5.0 pyasn1-modules 0.3.0 pycocotools 2.0.6 pycparser 2.21 pyct 0.5.0 pydantic 1.10.7 pydata-google-auth 1.7.0 pydot 1.4.2 pydot-ng 2.0.0 pydotplus 2.0.2 PyDrive 1.3.1 pyerfa 2.0.0.3 pyg-lib 0.2.0+pt20cu118 pygame 2.3.0 Pygments 2.14.0 PyGObject 3.36.0 pymc 5.1.2 PyMeeus 0.5.12 pymystem3 0.2.0 pynvml 11.5.0 PyOpenGL 3.1.6 pyparsing 3.0.9 pyrsistent 0.19.3 pyscf 2.2.1 PySocks 1.7.1 pytensor 2.10.1 pytest 7.1.2 pytest-cov 3.0.0 pytest-forked 1.6.0 pytest-xdist 2.5.0 python-apt 0.0.0 python-dateutil 2.8.2 python-louvain 0.16 python-slugify 8.0.1 python-utils 3.5.2 pytz 2022.7.1 pytz-deprecation-shim 0.1.0.post0 pyviz-comms 2.2.1 PyWavelets 1.4.1 PyYAML 6.0 pyzmq 23.2.1 qdldl 0.1.7 qudida 0.0.4 rdkit-pypi 2022.9.5 regex 2022.10.31 requests 2.27.1 requests-oauthlib 1.3.1 requests-unixsocket 0.2.0 rich 13.3.4 rpy2 3.5.5 rsa 4.9 ruamel.yaml 0.17.21 ruamel.yaml.clib 0.2.7 scikit-image 0.19.3 scikit-learn 1.2.2 scipy 1.10.1 scs 3.2.3 seaborn 0.12.2 Send2Trash 1.8.0 setuptools 59.5.0 shap 0.41.0 shapely 2.0.1 six 1.16.0 sklearn-pandas 2.2.0 slicer 0.0.7 smart-open 6.3.0 sniffio 1.3.0 snowballstemmer 2.2.0 sortedcontainers 2.4.0 soundfile 0.12.1 soupsieve 2.4.1 soxr 0.3.5 spacy 3.5.2 spacy-legacy 3.0.12 spacy-loggers 1.0.4 Sphinx 5.3.0 sphinx-rtd-theme 1.0.0 sphinxcontrib-applehelp 1.0.4 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 2.0.1 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.5 SQLAlchemy 2.0.10 sqlparse 0.4.4 srsly 2.4.6 statsmodels 0.13.5 sympy 1.11.1 tables 3.8.0 tabulate 0.8.10 tblib 1.7.0 tenacity 8.2.2 tensorboard 2.8.0 tensorboard-data-server 0.6.1 tensorboard-plugin-wit 1.8.1 tensorflow 2.12.0 tensorflow-datasets 4.8.3 tensorflow-estimator 2.12.0 tensorflow-gcs-config 2.12.0 tensorflow-hub 0.13.0 tensorflow-io-gcs-filesystem 0.32.0 tensorflow-metadata 1.13.1 tensorflow-probability 0.19.0 tensorstore 0.1.36 termcolor 2.3.0 terminado 0.17.1 text-unidecode 1.3 textblob 0.17.1 tf-slim 1.1.0 thinc 8.1.9 threadpoolctl 3.1.0 tifffile 2023.4.12 tinycss2 1.2.1 toml 0.10.2 tomli 2.0.1 toolz 0.12.0 torch 2.0.0+cu118 torch-cluster 1.6.1+pt20cu118 torch-geometric 2.3.1 torch-scatter 2.1.1+pt20cu118 torch-sparse 0.6.17+pt20cu118 torch-spline-conv 1.2.2+pt20cu118 torchaudio 2.0.1+cu118 torchdata 0.6.0 torchsummary 1.5.1 torchtext 0.15.1 torchvision 0.15.1+cu118 tornado 6.2 tqdm 4.64.0 traitlets 5.7.1 triton 2.0.0 tweepy 4.13.0 typed-argument-parser 1.7.2 typer 0.7.0 typing_extensions 4.5.0 typing-inspect 0.8.0 tzdata 2023.3 tzlocal 4.3 uritemplate 4.1.1 urllib3 1.26.15 vega-datasets 0.9.0 wasabi 1.1.1 wcwidth 0.2.6 webcolors 1.13 webencodings 0.5.1 websocket-client 1.5.1 Werkzeug 2.3.0 wheel 0.40.0 widgetsnbextension 3.6.4 wordcloud 1.8.2.2 wrapt 1.14.1 xarray 2022.12.0 xarray-einstats 0.5.1 xgboost 1.7.5 xlrd 2.0.1 yellowbrick 1.5 yfinance 0.2.18 zict 3.0.0 zipp 3.15.0

CM-BF commented 1 year ago

Hi @czstudio,

Thank you for your follow-up. The key problem is that there are some incompatible updates of torch-geometric as far as I know since it's version 2, and the explain_message might be their new parameter for explainability. Although we may update our project for "their compatibility problems" in the future, for now, I strongly encourage you to install these package versions: PyTorch (==1.10.1) with CUDA $\ge$ 11.3, PyG (==2.0.4), RDKit (==2020.09.5). Please let me know if any further questions. :)

Best, Shurui

czstudio commented 1 year ago

Thank you very much!! pip install torch_geometric==2.0.4 solved the problem. I will sort out a list in google colab that can be run directly and has comparative results.

CM-BF commented 1 year ago

You are most welcome! For other discussions, please open a new discussion or issue. Since the problem is solved, I will close this issue. :smile: