[BUG] autogl 0.1.1 is not compactible with torch-geometric 1.6.3

[iwatobipen]

Describe the bug
When I run the graph_classification.py code, I got following error.
How can I fix the error? Any advice will be greatly appreciated.
Thanks

`
~/src/AutoGL/examples$ python graph_classification.py

Traceback (most recent call last):
File "graph_classification.py", line 19, in
cv_split=10,
File "/home/user/src/AutoGL/autogl/solver/classifier/graph_classifier.py", line 294, in fit
self.feature_module.fit(dataset.train_split)
File "/home/user/src/AutoGL/autogl/module/feature/base.py", line 116, in fit
dataset = self._rebuild(dataset, _dataset)
File "/home/user/src/AutoGL/autogl/module/feature/base.py", line 57, in _rebuild
data, slices = dataset.collate(datalist)
File "/home/user/miniconda3/envs/grapl/lib/python3.7/site-packages/torch_geometric/data/in_memory_dataset.py", line 128, in collate
dim=data.cat_dim(key, item))
RuntimeError: Sizes of tensors must match except in dimension 0. Got 1 and 2 in dimension 1 (The offending index is 5)

`

Environment (please complete the following information):

• OS: [Ubuntu20.04]
• python version: [Python 3.7.9]
• autogl version: [0.1.1]

[Frozenmad]

Thanks for your bug information. We will come back to you later after investigation.

[Frozenmad]

I've test the graph classification example under python 3.6.10 and autogl 0.1.1 and cannot reproduce the bug. Can you provide more information about the package you have installed? [output of pip list] @iwatobipen

[iwatobipen]

Thanks for your prompt reply. Here is my list.
Thanks

Package Version Location

---

alabaster 0.7.12
alembic 1.4.3
altair 4.1.0
AmberLite 16.0
AmberTools 17.0
anaconda-client 1.7.2
appdirs 1.4.4
argh 0.26.2
argon2-cffi 20.1.0
ase 3.20.1
asn1crypto 1.4.0
astor 0.8.1
async-generator 1.10
atomicwrites 1.4.0
attrs 20.3.0
auto-graph-learning 0.1.1 /home/iwatobipen/src/AutoGL
Babel 2.9.0
backcall 0.2.0
base58 2.0.1
bayesian-optimization 1.2.0
beautifulsoup4 4.9.3
biopandas 0.2.7
biopython 1.78
bleach 3.2.1
blinker 1.4
blis 0.4.1
boto 2.49.0
boto3 1.16.42
botocore 1.19.42
brotlipy 0.7.0
cached-property 1.5.2
cachetools 4.1.1
catalogue 1.0.0
catboost 0.24.3
certifi 2020.12.5
cffi 1.14.4
chardet 4.0.0
chart-studio 1.1.0
chocolate 0.0.2
click 7.1.2
cloudpickle 1.6.0
clyent 1.2.2
colorama 0.4.4
colorlover 0.3.0
conda 4.9.2
conda-build 3.20.5
conda-package-handling 1.7.2
configparser 5.0.1
confuse 1.4.0
cryptography 3.3.1
cufflinks 0.17.3
cycler 0.10.0
cymem 2.0.4
Cython 0.29.21
cytoolz 0.11.0
dask 2020.12.0
databricks-cli 0.9.1
dataclasses 0.6
datefinder 0.7.1
decorator 4.4.2
deepdiff 5.0.2
defusedxml 0.6.0
dill 0.3.3
distro 1.5.0
docker 4.4.0
docker-pycreds 0.4.0
docopt 0.6.2
docutils 0.15.2
entrypoints 0.3
fastjsonschema 2.14.5
filelock 3.0.12
Flask 1.1.2
funcy 1.15
future 0.18.2
gensim 3.8.0
gitdb 4.0.5
GitPython 3.1.11
glob2 0.7
gorilla 0.3.0
gunicorn 20.0.4
h5py 2.8.0
htmlmin 0.1.12
hyperopt 0.2.5
idna 2.10
imagecodecs 2020.5.30
ImageHash 4.2.0
imageio 2.9.0
imagesize 1.2.0
importlib-metadata 2.0.0
importlib-resources 3.3.1
ipykernel 5.3.4
ipython 7.19.0
ipython-genutils 0.2.0
ipywidgets 7.5.1
isodate 0.6.0
itsdangerous 1.1.0
Jinja2 2.11.2
jmespath 0.10.0
joblib 1.0.0
jsonpickle 1.4.2
jsonschema 3.0.2
jupyter 1.0.0
jupyter-client 6.1.7
jupyter-console 6.2.0
jupyter-contrib-core 0.3.3
jupyter-contrib-nbextensions 0.5.1
jupyter-core 4.7.0
jupyter-highlight-selected-word 0.2.0
jupyter-latex-envs 1.4.6
jupyter-nbextensions-configurator 0.4.1
jupyterlab-pygments 0.1.2
kiwisolver 1.3.0
kmodes 0.10.2
libarchive-c 2.9
lightgbm 3.1.1
littleutils 0.2.2
llvmlite 0.34.0
lxml 4.6.2
Mako 1.1.3
MarkupSafe 1.1.1
matplotlib 3.3.2
missingno 0.4.2
mistune 0.8.4
mkl-fft 1.2.0
mkl-random 1.1.1
mkl-service 2.3.0
mlxtend 0.18.0
modeller 0.1.1
more-itertools 8.6.0
msgpack 1.0.1
murmurhash 1.0.5
nbclient 0.5.1
nbconvert 6.0.7
nbformat 5.0.8
nest-asyncio 1.4.3
NetLSD 1.0.2
networkx 2.5
nglview 2.7.7
nltk 3.5
notebook 6.1.5
numba 0.51.2
numexpr 2.7.1
numpy 1.19.2
ogb 1.2.4
olefile 0.46
openforcefields 1.3.0
OpenMM 7.5.0
ordered-set 4.0.2
outdated 0.2.0
packaging 20.8
packmol-memgen 1.0.5rc0
pandas 1.1.5
pandas-profiling 2.9.0
pandocfilters 1.4.3
ParmEd 3.2.0
parso 0.8.1
pathtools 0.1.2
patsy 0.5.1
pdb4amber 1.7.dev0
pexpect 4.8.0
phik 0.10.0
pickleshare 0.7.5
pigeonXT-jupyter 0.4.1
Pillow 8.0.1
Pint 0.16.1
pip 20.3.3
pipreqs 0.4.10
pkginfo 1.6.1
plac 1.1.0
plotly 4.14.1
pluggy 0.13.1
Pmw 2.0.1
preshed 3.0.2
progressbar2 3.53.1
prometheus-client 0.9.0
prompt-toolkit 3.0.8
protobuf 3.14.0
psutil 5.7.3
ptyprocess 0.6.0
py 1.10.0
pyarrow 2.0.0
pycairo 1.19.1
pycaret 2.1.2
pycosat 0.6.3
pycparser 2.20
pydantic 1.7.3
pydeck 0.5.0
Pygments 2.7.3
pyLDAvis 2.1.2
pymbar 3.0.5
pymol 2.5.0a0
pyMSMT 19.0
pyod 0.8.4
PyOpenGL 3.1.1a1
pyOpenSSL 20.0.1
pyparsing 2.4.7
PyQt5 5.12.3
PyQt5-sip 4.19.18
PyQtChart 5.12
PyQtWebEngine 5.12.1
pyreadline 2.1
pyrsistent 0.17.3
PySocks 1.7.1
pytest 4.6.4
python-dateutil 2.8.1
python-editor 1.0.4
python-louvain 0.15
python-utils 2.4.0
pytraj 2.0.5
pytz 2020.4
PyWavelets 1.1.1
PyYAML 5.3.1
pyzmq 20.0.0
qcelemental 0.17.0
qtconsole 4.7.7
QtPy 1.9.0
querystring-parser 1.2.4
rdflib 5.0.0
readline 6.2.4.1
regex 2020.11.13
reportlab 3.5.51
requests 2.25.1
retrying 1.3.3
ruamel-yaml 0.15.87
s3transfer 0.3.3
sander 16.0
scikit-build 0.11.1
scikit-image 0.17.2
scikit-learn 0.23.2
scipy 1.5.2
seaborn 0.11.1
Send2Trash 1.5.0
setuptools 51.0.0.post20201207
shap 0.36.0
simplejson 3.17.2
six 1.15.0
slicer 0.0.7
smart-open 1.8.0
smmap 3.0.4
snowballstemmer 2.0.0
soupsieve 2.1
spacy 2.3.5
Sphinx 3.4.1
sphinx-rtd-theme 0.5.0
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 1.0.3
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.4
SQLAlchemy 1.3.21
sqlparse 0.4.1
srsly 1.0.5
statsmodels 0.12.1
streamlit 0.73.1
tabulate 0.8.7
tangled-up-in-unicode 0.0.6
terminado 0.9.1
testpath 0.4.4
textblob 0.15.3
thinc 7.4.5
threadpoolctl 2.1.0
tifffile 2020.12.8
toml 0.10.2
toolz 0.11.1
torch 1.7.0
torch-cluster 1.5.8
torch-geometric 1.6.3
torch-scatter 2.0.5
torch-sparse 0.6.8
torch-spline-conv 1.2.0
torchaudio 0.7.0a0+ac17b64
torchvision 0.8.1
tornado 6.1
tqdm 4.54.1
traitlets 5.0.5
typing-extensions 3.7.4.3
tzlocal 2.1
umap-learn 0.4.6
urllib3 1.25.11
validators 0.18.2
visions 0.5.0
wasabi 0.8.0
watchdog 1.0.2
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 0.57.0
Werkzeug 1.0.1
wheel 0.36.2
widgetsnbextension 3.5.1
wordcloud 1.8.1
xgboost 1.3.0
yarg 0.1.9
yellowbrick 1.2
zipp 3.4.0

[Frozenmad]

Thanks for your info. I've done some tests and find that the autogl=0.1.1 is not compactable with torch-geometric>1.6.1. We'll fix the bug in the future version of autogl to support up-to-date torch-geometric package.

For now, you can just lower your pytorch geometric package by:

pip install torch-goemtric==1.6.1

Thanks again for your info!

[iwatobipen]

I confirmed. The code worked with torch-geometric 1.6.1.
Thanks for your kind support and nice work.