Cannot Import PyTorch Geometric

[techGIAN]

I just installed Pytorch Geometric, but I'm getting this error whenever I try importing torch_geometric. Any idea how this can be fixed?

OSError: /home/gcalix/miniconda3/envs/env1/lib/python3.7/site-packages/torch_sparse/_version.so: undefined symbol: _ZN3c1017RegisterOperators25checkSchemaAndRegisterOp_EONS0_7OptionsE

Thanks in advance!

[EdisonLeeeee]

This error is usually caused by using multiple PyTorch or multiple CUDA versions. You need to make sure the extensions (e.g., torch_sparse, torch_scatter) get compiled with the correct PyTorch and CUDA versions.

Similar issue that may help: #999

[EdisonLeeeee]

That's weird. Could you please show me how you installed them, and your environment such as the pytorch version?

[techGIAN]

I used this commands:

pip install torch-scatter -f https://data.pyg.org/whl/torch-1.12.0+cu116.html
pip install torch-sparse -f https://data.pyg.org/whl/torch-1.12.0+cu116.html
pip install torch-geometric

Pytorch version is 1.12.1. Here are the packages installed in my environment:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
antlr-python-runtime      4.9.3              pyhd8ed1ab_1    conda-forge
blas                      1.0                         mkl  
bottleneck                1.3.5            py37h7deecbd_0  
brotlipy                  0.7.0           py37h27cfd23_1003  
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2022.07.19           h06a4308_0  
certifi                   2022.6.15        py37h06a4308_0  
cffi                      1.15.1           py37h74dc2b5_0  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
cryptography              37.0.1           py37h9ce1e76_0  
cudatoolkit               11.6.0              hecad31d_10    conda-forge
ffmpeg                    4.2.2                h20bf706_0  
freetype                  2.11.0               h70c0345_0  
giflib                    5.2.1                h7b6447c_0  
gmp                       6.2.1                h295c915_3  
gnutls                    3.6.15               he1e5248_0  
googledrivedownloader     0.4                pyhd3deb0d_1    conda-forge
html5lib                  1.1                pyhd3eb1b0_0  
idna                      3.3                pyhd3eb1b0_0  
importlib-metadata        4.11.3           py37h06a4308_0  
intel-openmp              2021.4.0          h06a4308_3561  
isodate                   0.6.0              pyhd3eb1b0_1  
jinja2                    3.0.3              pyhd3eb1b0_0  
joblib                    1.1.0              pyhd3eb1b0_0  
jpeg                      9e                   h7f8727e_0  
lame                      3.100                h7b6447c_0  
lcms2                     2.12                 h3be6417_0  
ld_impl_linux-64          2.38                 h1181459_1  
lerc                      3.0                  h295c915_0  
libdeflate                1.8                  h7f8727e_5  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 11.2.0               h1234567_1  
libgfortran-ng            7.5.0               ha8ba4b0_17  
libgfortran4              7.5.0               ha8ba4b0_17  
libgomp                   11.2.0               h1234567_1  
libidn2                   2.3.2                h7f8727e_0  
libopus                   1.3.1                h7b6447c_0  
libpng                    1.6.37               hbc83047_0  
libstdcxx-ng              11.2.0               h1234567_1  
libtasn1                  4.16.0               h27cfd23_0  
libtiff                   4.4.0                hecacb30_0  
libunistring              0.9.10               h27cfd23_0  
libvpx                    1.7.0                h439df22_0  
libwebp                   1.2.2                h55f646e_0  
libwebp-base              1.2.2                h7f8727e_0  
lz4-c                     1.9.3                h295c915_1  
markupsafe                2.1.1            py37h7f8727e_0  
mkl                       2021.4.0           h06a4308_640  
mkl-service               2.4.0            py37h7f8727e_0  
mkl_fft                   1.3.1            py37hd3c417c_0  
mkl_random                1.2.2            py37h51133e4_0  
ncurses                   6.3                  h5eee18b_3  
nettle                    3.7.3                hbbd107a_1  
networkx                  2.6.3              pyhd3eb1b0_0  
ninja                     1.10.2               h06a4308_5  
ninja-base                1.10.2               hd09550d_5  
numexpr                   2.8.3            py37h807cd23_0  
numpy                     1.21.5           py37h6c91a56_3  
numpy-base                1.21.5           py37ha15fc14_3  
omegaconf                 2.2.2            py37h89c1867_0    conda-forge
openh264                  2.1.1                h4ff587b_0  
openssl                   1.1.1q               h7f8727e_0  
packaging                 21.3               pyhd3eb1b0_0  
pandas                    1.3.5            py37h8c16a72_0  
pillow                    9.2.0            py37hace64e9_1  
pip                       22.1.2           py37h06a4308_0  
pycparser                 2.21               pyhd3eb1b0_0  
pyopenssl                 22.0.0             pyhd3eb1b0_0  
pyparsing                 3.0.9            py37h06a4308_0  
pysocks                   1.7.1                    py37_1  
python                    3.7.13               h12debd9_0  
python-dateutil           2.8.2              pyhd3eb1b0_0  
python_abi                3.7                     2_cp37m    conda-forge
pytorch                   1.12.1          py3.7_cuda11.6_cudnn8.3.2_0    pytorch
pytorch-cpu               1.1.0            py37he1b5a44_0    conda-forge
pytorch-mutex             1.0                        cuda    pytorch
pytz                      2022.1           py37h06a4308_0  
pyyaml                    6.0              py37h7f8727e_1  
rdflib                    6.2.0              pyhd8ed1ab_0    conda-forge
readline                  8.1.2                h7f8727e_1  
requests                  2.28.1           py37h06a4308_0  
scikit-learn              1.0.2            py37h51133e4_1    anaconda
scipy                     1.7.3            py37hc147768_0    anaconda
setuptools                63.4.1           py37h06a4308_0  
six                       1.16.0             pyhd3eb1b0_1  
sqlite                    3.39.2               h5082296_0  
threadpoolctl             2.2.0              pyh0d69192_0  
tk                        8.6.12               h1ccaba5_0  
torch-geometric           2.1.0.post1              pypi_0    pypi
torch-scatter             2.0.9                    pypi_0    pypi
torch-sparse              0.6.15                   pypi_0    pypi
torchaudio                0.12.1               py37_cu116    pytorch
torchvision               0.13.1               py37_cu116    pytorch
tqdm                      4.64.0           py37h06a4308_0  
typing_extensions         4.3.0            py37h06a4308_0  
urllib3                   1.26.11          py37h06a4308_0  
webencodings              0.5.1                    py37_1  
wheel                     0.37.1             pyhd3eb1b0_0  
x264                      1!157.20191217       h7b6447c_0  
xz                        5.2.5                h7f8727e_1  
yaml                      0.2.5                h7b6447c_0  
zipp                      3.8.0            py37h06a4308_0  
zlib                      1.2.12               h5eee18b_3  
zstd                      1.5.2                ha4553b6_0

Thanks for looking into this!

[EdisonLeeeee]

It seems that your PyTorch was installed via Anaconda, but it might not be a perfect choice. Perhaps you need to install PyTorch via pip install? I am not pretty sure but I used pip and it always works.

See this answer

[techGIAN]

Yes, I used conda. I just tried with using pip for the installations and it now works. Thanks!

[EdisonLeeeee]

Glad to see that : )