OSError: /home ...~.../python3.10/site-packages/torch_cluster/_version_cuda.so: undefined symbol: _ZN3c1017RegisterOperatorsD1Ev

username: Mah_sa
cooked: <p>Hi. I have an environment with specific configuration created by conda create en. The configuration is as:</p>
<p>channels:</p>
<ul>
<li>pytorch</li>
<li>pyg</li>
<li>nvidia<br>
dependencies:</li>
<li>python=3.10</li>
<li>pytorch=2.0.1</li>
<li>torchvision=0.15.2</li>
<li>pytorch-cuda=11.8</li>
<li>pyg=2.3.1</li>
<li>pytorch-cluster=1.6.1</li>
<li>pip:
<ul>
<li>lightning[pytorch-extra]==2.0.9</li>
<li>numpy==1.26.0</li>
<li>pillow==10.0.1</li>
<li>scipy==1.11.3</li>
<li>pandas==1.5.3</li>
<li>matplotlib==3.8.0</li>
<li>opencv-python==4.8.1.78</li>
<li>pyvisgraph==0.2.1</li>
<li>shapely==1.8.5.post1</li>
<li>wandb==0.15.11<br>
When creating the env, the conda list(in the env) shows me the package lists as:</li>
</ul>
</li>
</ul>
<h1><a name="packages-in-environment-at-home-miniconda3envs-1" class="anchor" href="#packages-in-environment-at-home-miniconda3envs-1"></a>packages in environment at /home/… /miniconda3/envs/…</h1>
<h1><a name="h-2" class="anchor" href="#h-2"></a></h1>
<h1><a name="name-version-build-channel-3" class="anchor" href="#name-version-build-channel-3"></a>Name                    Version                   Build  Channel</h1>
<p>_libgcc_mutex             0.1                        main<br>
_openmp_mutex             5.1                       1_gnu<br>
aiohttp                   3.9.5                    pypi_0    pypi<br>
aiosignal                 1.3.1                    pypi_0    pypi<br>
annotated-types           0.7.0                    pypi_0    pypi<br>
antlr4-python3-runtime    4.9.3                    pypi_0    pypi<br>
anyio                     4.4.0                    pypi_0    pypi<br>
appdirs                   1.4.4                    pypi_0    pypi<br>
arrow                     1.3.0                    pypi_0    pypi<br>
async-timeout             4.0.3                    pypi_0    pypi<br>
attrs                     23.2.0                   pypi_0    pypi<br>
backoff                   2.2.1                    pypi_0    pypi<br>
beautifulsoup4            4.12.3                   pypi_0    pypi<br>
blas                      1.0                         mkl<br>
blessed                   1.20.0                   pypi_0    pypi<br>
boto3                     1.34.140                 pypi_0    pypi<br>
botocore                  1.34.140                 pypi_0    pypi<br>
brotli-python             1.0.9           py310h6a678d5_8<br>
bzip2                     1.0.8                h5eee18b_6<br>
ca-certificates           2024.3.11            h06a4308_0<br>
certifi                   2024.6.2        py310h06a4308_0<br>
charset-normalizer        2.0.4              pyhd3eb1b0_0<br>
click                     8.1.7                    pypi_0    pypi<br>
contourpy                 1.2.1                    pypi_0    pypi<br>
croniter                  1.4.1                    pypi_0    pypi<br>
cuda-cudart               11.8.89                       0    nvidia<br>
cuda-cupti                11.8.87                       0    nvidia<br>
cuda-libraries            11.8.0                        0    nvidia<br>
cuda-nvrtc                11.8.89                       0    nvidia<br>
cuda-nvtx                 11.8.86                       0    nvidia<br>
cuda-runtime              11.8.0                        0    nvidia<br>
cuda-version              12.5                          3    nvidia<br>
cycler                    0.12.1                   pypi_0    pypi<br>
dateutils                 0.6.12                   pypi_0    pypi<br>
deepdiff                  7.0.1                    pypi_0    pypi<br>
dnspython                 2.6.1                    pypi_0    pypi<br>
docker-pycreds            0.4.0                    pypi_0    pypi<br>
docstring-parser          0.16                     pypi_0    pypi<br>
editor                    1.6.6                    pypi_0    pypi<br>
email-validator           2.2.0                    pypi_0    pypi<br>
exceptiongroup            1.2.1                    pypi_0    pypi<br>
fastapi                   0.111.0                  pypi_0    pypi<br>
fastapi-cli               0.0.4                    pypi_0    pypi<br>
ffmpeg                    4.3                  hf484d3e_0    pytorch<br>
filelock                  3.13.1          py310h06a4308_0<br>
fonttools                 4.53.1                   pypi_0    pypi<br>
freetype                  2.12.1               h4a9f257_0<br>
frozenlist                1.4.1                    pypi_0    pypi<br>
gitdb                     4.0.11                   pypi_0    pypi<br>
gitpython                 3.1.43                   pypi_0    pypi<br>
gmp                       6.2.1                h295c915_3<br>
gmpy2                     2.1.2           py310heeb90bb_0<br>
gnutls                    3.6.15               he1e5248_0<br>
h11                       0.14.0                   pypi_0    pypi<br>
httpcore                  1.0.5                    pypi_0    pypi<br>
httptools                 0.6.1                    pypi_0    pypi<br>
httpx                     0.27.0                   pypi_0    pypi<br>
hydra-core                1.3.2                    pypi_0    pypi<br>
idna                      3.7             py310h06a4308_0<br>
importlib-resources       6.4.0                    pypi_0    pypi<br>
inquirer                  3.3.0                    pypi_0    pypi<br>
intel-openmp              2023.1.0         hdb19cb5_46306<br>
itsdangerous              2.2.0                    pypi_0    pypi<br>
jinja2                    3.1.4           py310h06a4308_0<br>
jmespath                  1.0.1                    pypi_0    pypi<br>
joblib                    1.4.2           py310h06a4308_0<br>
jpeg                      9e                   h5eee18b_1<br>
jsonargparse              4.24.1                   pypi_0    pypi<br>
kiwisolver                1.4.5                    pypi_0    pypi<br>
lame                      3.100                h7b6447c_0<br>
lcms2                     2.12                 h3be6417_0<br>
ld_impl_linux-64          2.38                 h1181459_1<br>
lerc                      3.0                  h295c915_0<br>
libcublas                 11.11.3.6                     0    nvidia<br>
libcufft                  10.9.0.58                     0    nvidia<br>
libcufile                 1.10.0.4                      0    nvidia<br>
libcurand                 10.3.6.39                     0    nvidia<br>
libcusolver               11.4.1.48                     0    nvidia<br>
libcusparse               11.7.5.86                     0    nvidia<br>
libdeflate                1.17                 h5eee18b_1<br>
libffi                    3.4.4                h6a678d5_1<br>
libgcc-ng                 11.2.0               h1234567_1<br>
libgfortran-ng            11.2.0               h00389a5_1<br>
libgfortran5              11.2.0               h1234567_1<br>
libgomp                   11.2.0               h1234567_1<br>
libiconv                  1.16                 h5eee18b_3<br>
libidn2                   2.3.4                h5eee18b_0<br>
libnpp                    11.8.0.86                     0    nvidia<br>
libnvjpeg                 11.9.0.86                     0    nvidia<br>
libpng                    1.6.39               h5eee18b_0<br>
libstdcxx-ng              11.2.0               h1234567_1<br>
libtasn1                  4.19.0               h5eee18b_0<br>
libtiff                   4.5.1                h6a678d5_0<br>
libunistring              0.9.10               h27cfd23_0<br>
libuuid                   1.41.5               h5eee18b_0<br>
libwebp-base              1.3.2                h5eee18b_0<br>
lightning                 2.0.9                    pypi_0    pypi<br>
lightning-cloud           0.5.70                   pypi_0    pypi<br>
lightning-utilities       0.11.3.post0             pypi_0    pypi<br>
lz4-c                     1.9.4                h6a678d5_1<br>
markdown-it-py            3.0.0                    pypi_0    pypi<br>
markupsafe                2.1.3           py310h5eee18b_0<br>
matplotlib                3.8.0                    pypi_0    pypi<br>
mdurl                     0.1.2                    pypi_0    pypi<br>
mkl                       2023.1.0         h213fc3f_46344<br>
mkl-service               2.4.0           py310h5eee18b_1<br>
mkl_fft                   1.3.8           py310h5eee18b_0<br>
mkl_random                1.2.4           py310hdb19cb5_0<br>
mpc                       1.1.0                h10f8cd9_1<br>
mpfr                      4.0.2                hb69a4c5_1<br>
mpmath                    1.3.0           py310h06a4308_0<br>
multidict                 6.0.5                    pypi_0    pypi<br>
ncurses                   6.4                  h6a678d5_0<br>
nettle                    3.7.3                hbbd107a_1<br>
networkx                  3.3             py310h06a4308_0<br>
numpy                     1.26.0                   pypi_0    pypi<br>
omegaconf                 2.3.0                    pypi_0    pypi<br>
opencv-python             4.8.1.78                 pypi_0    pypi<br>
openh264                  2.1.1                h4ff587b_0<br>
openjpeg                  2.4.0                h9ca470c_1<br>
openssl                   3.0.14               h5eee18b_0<br>
ordered-set               4.1.0                    pypi_0    pypi<br>
orjson                    3.10.6                   pypi_0    pypi<br>
packaging                 24.1                     pypi_0    pypi<br>
pandas                    1.5.3                    pypi_0    pypi<br>
pathtools                 0.1.2                    pypi_0    pypi<br>
pillow                    10.0.1                   pypi_0    pypi<br>
pip                       24.0            py310h06a4308_0<br>
protobuf                  4.25.3                   pypi_0    pypi<br>
psutil                    5.9.0           py310h5eee18b_0<br>
pybind11-abi              4                    hd3eb1b0_1<br>
pydantic                  2.1.1                    pypi_0    pypi<br>
pydantic-core             2.4.0                    pypi_0    pypi<br>
pyg                       2.3.1           py310_torch_2.0.0_cu118    pyg<br>
pygments                  2.18.0                   pypi_0    pypi<br>
pyjwt                     2.8.0                    pypi_0    pypi<br>
pyparsing                 3.0.9           py310h06a4308_0<br>
pysocks                   1.7.1           py310h06a4308_0<br>
python                    3.10.14              h955ad1f_1<br>
python-dotenv             1.0.1                    pypi_0    pypi<br>
python-multipart          0.0.9                    pypi_0    pypi<br>
pytorch                   2.0.1           py3.10_cuda11.8_cudnn8.7.0_0    pytorch<br>
pytorch-cluster           1.6.1           py310_torch_2.0.0_cu118    pyg<br>
pytorch-cuda              11.8                 h7e8668a_5    pytorch<br>
pytorch-lightning         2.3.2                    pypi_0    pypi<br>
pytorch-mutex             1.0                        cuda    pytorch<br>
pytz                      2024.1                   pypi_0    pypi<br>
pyyaml                    6.0.1                    pypi_0    pypi<br>
readchar                  4.1.0                    pypi_0    pypi<br>
readline                  8.2                  h5eee18b_0<br>
requests                  2.32.2          py310h06a4308_0<br>
rich                      13.7.1                   pypi_0    pypi<br>
runs                      1.2.2                    pypi_0    pypi<br>
s3transfer                0.10.2                   pypi_0    pypi<br>
scikit-learn              1.4.2           py310h1128e8f_1<br>
scipy                     1.11.3                   pypi_0    pypi<br>
sentry-sdk                2.8.0                    pypi_0    pypi<br>
setproctitle              1.3.3                    pypi_0    pypi<br>
setuptools                69.5.1          py310h06a4308_0<br>
shapely                   1.8.5.post1              pypi_0    pypi<br>
shellingham               1.5.4                    pypi_0    pypi<br>
six                       1.16.0                   pypi_0    pypi<br>
smmap                     5.0.1                    pypi_0    pypi<br>
sniffio                   1.3.1                    pypi_0    pypi<br>
soupsieve                 2.5                      pypi_0    pypi<br>
sqlite                    3.45.3               h5eee18b_0<br>
starlette                 0.37.2                   pypi_0    pypi<br>
starsessions              1.3.0                    pypi_0    pypi<br>
sympy                     1.12            py310h06a4308_0<br>
tbb                       2021.8.0             hdb19cb5_0<br>
tensorboardx              2.6.2.2                  pypi_0    pypi<br>
threadpoolctl             3.5.0           py310h2f386ee_0<br>
tk                        8.6.14               h39e8969_0<br>
torchmetrics              1.4.0.post0              pypi_0    pypi<br>
torchtriton               2.0.0                     py310    pytorch<br>
torchvision               0.15.2              py310_cu118    pytorch<br>
tqdm                      4.66.4          py310h2f386ee_0<br>
traitlets                 5.14.3                   pypi_0    pypi<br>
typer                     0.12.3                   pypi_0    pypi<br>
types-python-dateutil     2.9.0.20240316           pypi_0    pypi<br>
typeshed-client           2.5.1                    pypi_0    pypi<br>
typing_extensions         4.11.0          py310h06a4308_0<br>
tzdata                    2024a                h04d1e81_0<br>
ujson                     5.10.0                   pypi_0    pypi<br>
urllib3                   2.2.2           py310h06a4308_0<br>
uvicorn                   0.30.1                   pypi_0    pypi<br>
uvloop                    0.19.0                   pypi_0    pypi<br>
wandb                     0.15.11                  pypi_0    pypi<br>
watchfiles                0.22.0                   pypi_0    pypi<br>
wcwidth                   0.2.13                   pypi_0    pypi<br>
websocket-client          1.8.0                    pypi_0    pypi<br>
websockets                12.0                     pypi_0    pypi<br>
wheel                     0.43.0          py310h06a4308_0<br>
xmod                      1.8.1                    pypi_0    pypi<br>
xz                        5.4.6                h5eee18b_1<br>
yarl                      1.9.4                    pypi_0    pypi<br>
zlib                      1.2.13               h5eee18b_1<br>
zstd                      1.5.5                hc292b87_2</p>
<p>When executing the code i have this error:</p>
<p>oserror:%20/home/… lib/python3.10/site-packages/torch_cluster/_version_cuda…so: undefined symbol: _ZN3c1017RegisterOperatorsD1Ev</p>
<p>When I uninstall torch-cluster, it works for a bit longer but stops when the code needs it.</p>
<p>Would you please help me with that?</p>

username: ptrblck
cooked: <p>Your <code>torch-cluster</code> version might not be compatible with your PyTorch installation.<br>
I don’t know if and where a support matrix between these libs is shared.</p>