search

pyg-team / pytorch_geometric

Graph Neural Network Library for PyTorch
https://pyg.org
MIT License
20.91k stars 3.61k forks source link

can't run with this error: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs #3836

Open xyang2316 opened 2 years ago

xyang2316 commented 2 years ago

😵 Installation

Hi!

I installed the PyG according to the documentation(https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html). tried to run some sample code to test if I installed successfully, then I encountered this issue.

Traceback (most recent call last): File "test_dataloader.py", line 54, in from torch_geometric.data import Data File "/usr/local/lib/python3.8/dist-packages/torch_geometric/init.py", line 4, in import torch_geometric.data File "/usr/local/lib/python3.8/dist-packages/torch_geometric/data/init.py", line 1, in from .data import Data File "/usr/local/lib/python3.8/dist-packages/torch_geometric/data/data.py", line 3, in from torch_geometric.typing import OptTensor, NodeType, EdgeType File "/usr/local/lib/python3.8/dist-packages/torch_geometric/typing.py", line 4, in from torch_sparse import SparseTensor File "/usr/local/lib/python3.8/dist-packages/torch_sparse/init.py", line 15, in torch.ops.load_library(importlib.machinery.PathFinder().find_spec( File "/usr/lib/python3/dist-packages/torch/_ops.py", line 104, in load_library ctypes.CDLL(path) File "/usr/lib/python3.8/ctypes/init.py", line 373, in init self._handle = _dlopen(self._name, mode)

OSError: /usr/local/lib/python3.8/dist-packages/torch_sparse/_version_cuda.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

I tried to search previous issues, there is someplace mentioned about that system cuda and PyTorch cuda mismatch. I check mine, they both at 11.1, so I think it may not be the root cause of my issue.

Can anyone help me with this? Is there any other possibility? I have been stuck here for 4 days and have no clue about next move. Thank you so much for any advice!

Environment

Additional context

rusty1s commented 2 years ago

How did you install PyTorch in the first place? Are you using the official version from pytorch.org?

xyang2316 commented 2 years ago

Yes, the Pytorch was installed from the official site.

rusty1s commented 2 years ago

Which Linux distribution are you using in particular? There seems to exist some weird behavior in the latest wheel on some Linux distros, which I haven't figured out yet how to resolve. Can you check if installing from source helps to resolve this?

pip install --verbose torch-scatter
pip install --verbose torch-sparse

(might take some time to finish)

xyang2316 commented 2 years ago

I just installed a conda environment and tried to install these from source. But the installation failed. torch-scatter seems fine, it failed on torch-sparse. Here is the error: ERROR: Command errored out with exit status 1: /home/labcluster/anaconda3/envs/xy/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-vl9eon56/torch-sparse_66dc1c303ebf4b4eadeb75b03fde6685/setup.py'"'"'; __file__='"'"'/tmp/pip-install-vl9eon56/torch-sparse_66dc1c303ebf4b4eadeb75b03fde6685/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ldw4iria/install-record.txt --single-version-externally-managed --compile --install-headers /home/labcluster/anaconda3/envs/xy/include/python3.9/torch-sparse Check the logs for full command output.

I am currently using the conda environment and here is my updated the system: PyG version (torch_geometric.version): N/A PyTorch version: (torch.version): 1.11.0.dev20220116 OS (e.g., Linux): Linux Python version (e.g., 3.9): Python 3.9.7 CUDA/cuDNN version: cuda 11.1 (nvcc version also 11.1) How you installed PyTorch and PyG (conda, pip, source): conda install pytorch torchvision cudatoolkit=11 -c pytorch-nightly Any other relevant information (e.g., version of torch-scatter):

I also tried to install PyG from conda(conda install pyg -c pyg -c conda-forge), but it still shows the same error as before(ZN5torch3jit17parseSchemaOrNameERKSs). Please help me with this. Thank you so much!

rusty1s commented 2 years ago

We do not provide binaries yet for PyTorch 1.10. Installing via

conda install pytorch cudatoolkit=11 -c pytorch
conda install pyg -c pyg -c conda-forge

is likely able to fix these issues for you. If you desperately want to use PyTorch 1.11 nightly, you have to install torch-scatter and torch-sparse from source:

pip install --verbose torch-scatter torch-sparse torch-geometric
xyang2316 commented 2 years ago

It is the lab's environment, and they said the PyTorch 1.11 nightly is the one that compatible with the CUDA. I tried to install from the source, it occurs error as follow:

ERROR: Command errored out with exit status 1: /home/labcluster/anaconda3/envs/xy/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qoy_q2gx/torch-sparse_06f477d8cfdd433e95bf235c250f3297/setup.py'"'"'; file='"'"'/tmp/pip-install-qoy_q2gx/torch-sparse_06f477d8cfdd433e95bf235c250f3297/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-9adwdi3t/install-record.txt --single-version-externally-managed --compile --install-headers /home/labcluster/anaconda3/envs/xy/include/python3.9/torch-sparse Check the logs for full command output.

Any idea about this? Thank you for your help.

rusty1s commented 2 years ago

You may need to link the full log of

pip install --verbose torch-scatter
ucasiggcas commented 2 years ago

I got the same error by using the codes

conda install pytorch cudatoolkit=10.1 -c pytorch
conda install pyg -c pyg -c conda-forge

Traceback (most recent call last): File "/..y", line 2, in from torch_geometric.datasets import TUDataset File "..python3.9/site-packages/torch_geometric/init.py", line 7, in import torch_geometric.data File "..python3.9/site-packages/torch_geometric/data/init.py", line 1, in from .data import Data File "..python3.9/site-packages/torch_geometric/data/data.py", line 3, in from torch_geometric.typing import OptTensor File "/../python3.9/site-packages/torch_geometric/typing.py", line 4, in from torch_sparse import SparseTensor File "/..python3.9/site-packages/torch_sparse/init.py", line 15, in torch.ops.load_library(importlib.machinery.PathFinder().find_spec( File "/..python3.9/site-packages/torch/_ops.py", line 104, in load_library ctypes.CDLL(path) File "/..python3.9/ctypes/init.py", line 382, in init self._handle = _dlopen(self._name, mode) OSError: /.../python3.9/site-packages/torch_sparse/_version_cpu.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

rusty1s commented 2 years ago

Can you show me the output of conda list?

faye33 commented 2 years ago

@rusty1s Hello... I have been tortured by the same error today: "OSError: /....../site-packages/torch_scatter/_version.so: undefined symbol:_ZN3c105ErrorC1ENS_14SourceLocationERKSs"

Some told it's because more than one pytorch version exists in the environment, so I tried to recreate an environment and reinstall pytorch via downloaded package. But it still occurs...

Below is the output of conda list in my environment, please have a look.

Name                    Version                   Build  Channel

-- _libgcc_mutex             0.1                        main    defaults addict                    2.4.0                    pypi_0    pypi anyio                     3.5.0                    pypi_0    pypi argon2-cffi               21.3.0                   pypi_0    pypi argon2-cffi-bindings      21.2.0                   pypi_0    pypi attrs                     21.4.0                   pypi_0    pypi babel                     2.9.1                    pypi_0    pypi backcall                  0.2.0                    pypi_0    pypi bleach                    4.1.0                    pypi_0    pypi ca-certificates           2022.2.1             h06a4308_0    defaults certifi                   2021.10.8        py37h06a4308_2    defaults cffi                      1.15.0                   pypi_0    pypi charset-normalizer        2.0.12                   pypi_0    pypi cycler                    0.11.0                   pypi_0    pypi debugpy                   1.5.1                    pypi_0    pypi decorator                 5.1.1                    pypi_0    pypi defusedxml                0.7.1                    pypi_0    pypi deprecation               2.1.0                    pypi_0    pypi entrypoints               0.4                      pypi_0    pypi fonttools                 4.29.1                   pypi_0    pypi future                    0.18.2                   pypi_0    pypi googledrivedownloader     0.4                      pypi_0    pypi idna                      3.3                      pypi_0    pypi imageio                   2.16.1                   pypi_0    pypi importlib-metadata        4.11.2                   pypi_0    pypi importlib-resources       5.4.0                    pypi_0    pypi ipykernel                 6.9.1                    pypi_0    pypi ipython                   7.32.0                   pypi_0    pypi ipython-genutils          0.2.0                    pypi_0    pypi ipywidgets                7.6.5                    pypi_0    pypi isodate                   0.6.1                    pypi_0    pypi jedi                      0.18.1                   pypi_0    pypi jinja2                    3.0.3                    pypi_0    pypi joblib                    1.1.0                    pypi_0    pypi json5                     0.9.6                    pypi_0    pypi jsonschema                4.4.0                    pypi_0    pypi jupyter-client            7.1.2                    pypi_0    pypi jupyter-core              4.9.2                    pypi_0    pypi jupyter-packaging         0.11.1                   pypi_0    pypi jupyter-server            1.13.5                   pypi_0    pypi jupyterlab                3.3.0                    pypi_0    pypi jupyterlab-pygments       0.1.2                    pypi_0    pypi jupyterlab-server         2.10.3                   pypi_0    pypi jupyterlab-widgets        1.0.2                    pypi_0    pypi kiwisolver                1.3.2                    pypi_0    pypi libedit                   3.1.20210910         h7f8727e_0    defaults libffi                    3.2.1             hf484d3e_1007    defaults libgcc-ng                 9.1.0                hdf63c60_0    defaults libstdcxx-ng              9.3.0               hd4cf53a_17    defaults markupsafe                2.1.0                    pypi_0    pypi matplotlib                3.2.2                    pypi_0    pypi matplotlib-inline         0.1.3                    pypi_0    pypi mistune                   0.8.4                    pypi_0    pypi nbclassic                 0.3.6                    pypi_0    pypi nbclient                  0.5.11                   pypi_0    pypi nbconvert                 6.4.2                    pypi_0    pypi nbformat                  5.1.3                    pypi_0    pypi ncurses                   6.3                  h7f8727e_2    defaults nest-asyncio              1.5.4                    pypi_0    pypi networkx                  2.6.3                    pypi_0    pypi notebook                  6.4.8                    pypi_0    pypi notebook-shim             0.1.0                    pypi_0    pypi numpy                     1.21.5                   pypi_0    pypi open3d                    0.15.2                   pypi_0    pypi opencv-python             4.5.5.62                 pypi_0    pypi openssl                   1.0.2u               h7b6447c_0    defaults packaging                 21.3                     pypi_0    pypi pandas                    1.1.5                    pypi_0    pypi pandocfilters             1.5.0                    pypi_0    pypi parso                     0.8.3                    pypi_0    pypi pexpect                   4.8.0                    pypi_0    pypi pickleshare               0.7.5                    pypi_0    pypi pillow                    8.3.2                    pypi_0    pypi pip                       21.2.2           py37h06a4308_0    defaults prometheus-client         0.13.1                   pypi_0    pypi prompt-toolkit            3.0.28                   pypi_0    pypi ptyprocess                0.7.0                    pypi_0    pypi pycparser                 2.21                     pypi_0    pypi pygments                  2.11.2                   pypi_0    pypi pyparsing                 3.0.7                    pypi_0    pypi pyquaternion              0.9.9                    pypi_0    pypi pyrsistent                0.18.1                   pypi_0    pypi python                    3.7.0                h6e4f718_3    defaults python-dateutil           2.8.2                    pypi_0    pypi pytz                      2021.3                   pypi_0    pypi pywavelets                1.2.0                    pypi_0    pypi pyyaml                    6.0                      pypi_0    pypi pyzmq                     22.3.0                   pypi_0    pypi rdflib                    6.1.1                    pypi_0    pypi readline                  7.0                  h7b6447c_5    defaults requests                  2.27.1                   pypi_0    pypi scikit-image              0.15.0                   pypi_0    pypi scikit-learn              1.0.2                    pypi_0    pypi scipy                     1.7.3                    pypi_0    pypi send2trash                1.8.0                    pypi_0    pypi setuptools                58.0.4           py37h06a4308_0    defaults six                       1.16.0                   pypi_0    pypi sniffio                   1.2.0                    pypi_0    pypi sqlite                    3.33.0               h62c20be_0    defaults terminado                 0.13.2                   pypi_0    pypi testpath                  0.6.0                    pypi_0    pypi threadpoolctl             3.1.0                    pypi_0    pypi tk                        8.6.11               h1ccaba5_0    defaults tomlkit                   0.10.0                   pypi_0    pypi torch                     1.6.0                    pypi_0    pypi torch-cluster             1.5.7                    pypi_0    pypi torch-geometric           2.0.3                    pypi_0    pypi torch-scatter             2.0.5                    pypi_0    pypi torch-sparse              0.6.7                    pypi_0    pypi torch-spline-conv         1.2.0                    pypi_0    pypi torchvision               0.7.0                    pypi_0    pypi tornado                   6.1                      pypi_0    pypi tqdm                      4.63.0                   pypi_0    pypi traitlets                 5.1.1                    pypi_0    pypi typing-extensions         4.1.1                    pypi_0    pypi urllib3                   1.26.8                   pypi_0    pypi wcwidth                   0.2.5                    pypi_0    pypi webencodings              0.5.1                    pypi_0    pypi websocket-client          1.3.1                    pypi_0    pypi wheel                     0.37.1             pyhd3eb1b0_0    defaults widgetsnbextension        3.5.2                    pypi_0    pypi xz                        5.2.5                h7b6447c_0    defaults yacs                      0.1.8                    pypi_0    pypi zipp                      3.7.0                    pypi_0    pypi zlib                      1.2.11               h7f8727e_4    defaults

Any help would be appreciated!

rusty1s commented 2 years ago

It looks like both PyG and PyTorch are installed from pip (rather from conda), right? What commands did you run to install them?

faye33 commented 2 years ago

@rusty1s Thank you for your reply! In a new environment, I installed these packages via pip using pre-downloaded .whl files:

pytorch: pip install torch-1.6.0-cp37-cp37m-linux_x86_64.whl

torch-geometric: pip install torch_scatter-2.0.5+cu102-cp37-cp37m-linux_x86_64.whl pip install torch_spline_conv-1.2.0+cu102-cp37-cp37m-linux_x86_64.whl pip install torch_cluster-1.5.7+cu102-cp37-cp37m-linux_x86_64.whl pip intstall torch_sparse-0.6.7+cu102-cp37-cp37m-linux_x86_64.whl and finally pip intstall torch-geometric

rusty1s commented 2 years ago

Thank you! Interesting. I assume that the CPU/CUDA version between torch-1.6.0 and torch-scatter-2.0.5 match? Otherwise, this obviously might explain the issue. Any chance you can confirm that later releases, e.g., the newest ones for PyTorch 1.10 work for you instead? I doubt there is any chance for us to re-create the wheels for PyTorch 1.6 anyway. Furthermore, what happens if you do not pre-download the wheels and install via -f syntax?

faye33 commented 2 years ago

@rusty1s I followed version corresbondences on [https://pytorch-geometric.com/whl/], thus torch-1.6.0 and torch-scatter-2.0.5 should match. And your doubt about the 1.6 version of Pytorch is correct to some extent, cause that error does not occur when I use 1.4 . (chose 1.4 because my cuda version is 10.0, kind of old.) I will try Pytorch 1.10 as you suggested for testing and give an update later. Thank you.

faye33 commented 2 years ago

@rusty1s Hello!!!! I tested pytorch 1.10.0 whith cuda 10.2, the same as 1.4.0 ，the error did not happen!

rusty1s commented 2 years ago

Thanks for confirming. I hope you are good to go now.

yinyee commented 1 year ago

Hi @rusty1s I hope you can help -- been stuck on this for a while. I am encountering a similar error, even for a CPU-only build, when running import torch_geometric :

/opt/conda/lib/python3.10/site-packages/torch_cluster/_version_cpu.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

I am using a Dockerfile based on jupyter/scipy-notebook:

RUN conda update -n base conda && conda clean -afy

RUN conda install pytorch torchvision torchaudio cpuonly -c pytorch && conda clean -afy

RUN conda install pyg -c pyg && conda clean -afy

RUN conda install pytorch-scatter pytorch-sparse pytorch-cluster -c pyg && conda clean -afy

Here is an excerpt of conda list inside the Docker container:

pyg                       2.3.0           py310_torch_2.0.0_cpu    pyg
pygments                  2.15.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.6.0              pyhd8ed1ab_0    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3          py310h1fa729e_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.8.0           py310hde6a235_1    conda-forge
python                    3.10.10         he550d4f_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytorch                   2.0.0           cpu_py310hd11e9c7_0    conda-forge
pytorch-cluster           1.6.1           py310_torch_2.0.0_cpu    pyg
pytorch-mutex             1.0                         cpu    pytorch
pytorch-scatter           2.1.1           py310_torch_2.0.0_cpu    pyg
pytorch-sparse            0.6.17          py310_torch_2.0.0_cpu    pyg

I've checked https://pytorch-geometric.com/whl/torch-2.0.0%2Bcpu.html and it should work with the latest versions of everything.

I've also tried with CUDA 11.7 and it fails in the same way.

Additional context I am doing my development on Windows Subsystem for Linux.

rusty1s commented 1 year ago

The problem is that you install the PyTorch version from conda-forge, while you need the one from -c pytorch.

yinyee commented 1 year ago

Thanks @rusty1s -- I couldn't get conda to install from -c pytorch so ended up using pip for everything and it all worked perfectly.

P.S. My unsuccessful approach trying to force conda to use the pytorch channel was to run conda config --prepend channels pytorch before installing any packages (in case someone knows a better way)

mainguyenanhvu commented 4 months ago

I face the same issue. I install following these commands based on official guide, pytorch_official:

conda env create --file environment.yml
conda activate diffdock
conda install pytorch torchvision torchaudio pytorch-cuda=12.1 -c pytorch -c nvidia
conda install conda-forge::rdkit
pip install pyg_lib torch_geometric  torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.1.0+cu121.html

The enviroment.yml

name: diffdock
channels:
  - pyg
  - nvidia
  - pytorch
  - conda-forge
  - defaults
dependencies:
  - python=3.9.18
  - pip
  # Need to install torch in order to build openfold, so install it first
  - pip:
    - --extra-index-url https://download.pytorch.org/whl/cu117
    - --find-links https://pytorch-geometric.com/whl/torch-1.13.1+cu117.html
    - torch==1.13.1+cu117
  - pip:
    - --extra-index-url https://download.pytorch.org/whl/cu117
    - --find-links https://pytorch-geometric.com/whl/torch-1.13.1+cu117.html
    - dllogger @ git+https://github.com/NVIDIA/dllogger.git
    - e3nn==0.5.0
    - fair-esm[esmfold]==2.0.0
    - networkx==2.8.4
    - openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307
    - pandas==1.5.1
    - prody==2.2.0
    - prody==2.2.0
    - pybind11==2.11.1
    - rdkit==2022.03.3
    - scikit-learn==1.1.0
    - scipy==1.12.0
    - torch==1.13.1+cu117
    - torch-cluster==1.6.0+pt113cu117
    - torch-geometric==2.2.0
    - torch-scatter==2.1.0+pt113cu117
    - torch-sparse==0.6.16+pt113cu117
    - torch-spline-conv==1.2.1+pt113cu117
    - torchmetrics==0.11.0
  - pip:
    - gradio==3.50.*
    - requests

Error:

  File "/scratch/micromamba/envs/diffdock/lib/python3.9/site-packages/torch_geometric/nn/conv/__init__.py", line 8, in <module>
    from .gravnet_conv import GravNetConv
  File "/scratch/micromamba/envs/diffdock/lib/python3.9/site-packages/torch_geometric/nn/conv/gravnet_conv.py", line 13, in <module>
    from torch_cluster import knn
  File "/scratch/micromamba/envs/diffdock/lib/python3.9/site-packages/torch_cluster/__init__.py", line 18, in <module>
    torch.ops.load_library(spec.origin)
  File "/scratch/micromamba/envs/diffdock/lib/python3.9/site-packages/torch/_ops.py", line 852, in load_library
    ctypes.CDLL(path)
  File "/scratch/micromamba/envs/diffdock/lib/python3.9/ctypes/__init__.py", line 374, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: /scratch/micromamba/envs/diffdock/lib/python3.9/site-packages/torch_cluster/_version_cpu.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

Output of conda list:

#Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiofiles                  23.2.1                   pypi_0    pypi
aiohttp                   3.9.5                    pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
altair                    5.3.0                    pypi_0    pypi
annotated-types           0.6.0                    pypi_0    pypi
anyio                     4.3.0                    pypi_0    pypi
async-timeout             4.0.3                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
brotli-python             1.1.0            py39h3d6467e_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
cairo                     1.16.0            h35add3b_1015    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
chardet                   5.2.0            py39hf3d152e_1    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1            py39h7633fee_0    conda-forge
cuda-cudart               12.1.105                      0    nvidia
cuda-cupti                12.1.105                      0    nvidia
cuda-libraries            12.1.0                        0    nvidia
cuda-nvrtc                12.1.105                      0    nvidia
cuda-nvtx                 12.1.105                      0    nvidia
cuda-opencl               12.4.127                      0    nvidia
cuda-runtime              12.1.0                        0    nvidia
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0                    pypi_0    pypi
expat                     2.6.2                h59595ed_0    conda-forge
fastapi                   0.110.1                  pypi_0    pypi
ffmpeg                    4.3                  hf484d3e_0    pytorch
ffmpy                     0.3.2                    pypi_0    pypi
filelock                  3.13.4             pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_1    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.51.0           py39hd1e30aa_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
freetype-py               2.3.0              pyhd8ed1ab_0    conda-forge
frozenlist                1.4.1                    pypi_0    pypi
fsspec                    2024.3.1           pyhca7485f_0    conda-forge
gmp                       6.3.0                h59595ed_1    conda-forge
gmpy2                     2.1.2            py39h376b7d2_1    conda-forge
gnutls                    3.6.13               h85f3911_1    conda-forge
gradio                    3.50.2                   pypi_0    pypi
gradio-client             0.6.1                    pypi_0    pypi
greenlet                  3.0.3            py39h3d6467e_0    conda-forge
h11                       0.14.0                   pypi_0    pypi
httpcore                  1.0.5                    pypi_0    pypi
httpx                     0.27.0                   pypi_0    pypi
huggingface-hub           0.22.2                   pypi_0    pypi
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.7                pyhd8ed1ab_0    conda-forge
importlib-resources       6.4.0              pyhd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
jinja2                    3.1.3              pyhd8ed1ab_0    conda-forge
joblib                    1.4.0                    pypi_0    pypi
jpeg                      9e                   h166bdaf_2    conda-forge
jsonschema                4.21.1                   pypi_0    pypi
jsonschema-specifications 2023.12.1                pypi_0    pypi
kiwisolver                1.4.5            py39h7633fee_1    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.15                 hfd0df8a_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20230802.1      cxx17_h59595ed_0    conda-forge
libblas                   3.9.0           22_linux64_openblas    conda-forge
libboost                  1.82.0               h1bacd13_2    conda-forge
libboost-python           1.82.0           py39hda80f44_6    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcblas                  3.9.0           22_linux64_openblas    conda-forge
libcublas                 12.1.0.26                     0    nvidia
libcufft                  11.0.2.4                      0    nvidia
libcufile                 1.9.1.3                       0    nvidia
libcurand                 10.3.5.147                    0    nvidia
libcusolver               11.4.4.55                     0    nvidia
libcusparse               12.0.2.55                     0    nvidia
libdeflate                1.17                 h0b41bf4_0    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgfortran-ng            13.2.0               h69a702a_5    conda-forge
libgfortran5              13.2.0               ha4646dd_5    conda-forge
libglib                   2.80.0               hf2295e7_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             2.0.0                h9bf148f_0    pytorch
liblapack                 3.9.0           22_linux64_openblas    conda-forge
libnpp                    12.0.2.50                     0    nvidia
libnsl                    2.0.1                hd590300_0    conda-forge
libnvjitlink              12.1.105                      0    nvidia
libnvjpeg                 12.1.1.14                     0    nvidia
libopenblas               0.3.27          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.43               h2797004_0    conda-forge
libprotobuf               4.25.1               hf27288f_2    conda-forge
libsqlite                 3.45.2               h2797004_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libtiff                   4.5.0                h6adf6a1_2    conda-forge
libtorch                  2.1.2           cpu_generic_ha017de0_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.48.0               hd590300_0    conda-forge
libwebp-base              1.4.0                hd590300_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
markupsafe                2.1.5            py39hd1e30aa_0    conda-forge
matplotlib-base           3.8.4            py39he9076e7_0    conda-forge
mpc                       1.3.1                hfe3b2da_0    conda-forge
mpfr                      4.2.1                h9458935_1    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
multidict                 6.0.5                    pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.4.20240210         h59595ed_0    conda-forge
nettle                    3.6                  he412f7d_0    conda-forge
networkx                  3.2.1              pyhd8ed1ab_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
numpy                     1.26.4           py39h474f0d3_0    conda-forge
openh264                  2.1.1                h780b84a_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openssl                   3.2.1                hd590300_1    conda-forge
orjson                    3.10.1                   pypi_0    pypi
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pandas                    2.2.2            py39hddac248_0    conda-forge
pcre2                     10.43                hcad00b1_0    conda-forge
pillow                    10.3.0                   pypi_0    pypi
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
psutil                    5.9.8                    pypi_0    pypi
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycairo                   1.25.0           py39hc92de75_1    conda-forge
pydantic                  2.7.0                    pypi_0    pypi
pydantic-core             2.18.1                   pypi_0    pypi
pydub                     0.25.1                   pypi_0    pypi
pyg-lib                   0.4.0+pt21cu121          pypi_0    pypi
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.18          h0755675_1_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python-multipart          0.0.9                    pypi_0    pypi
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      4_cp39    conda-forge
pytorch                   2.1.2           cpu_generic_py39h3f191e9_3    conda-forge
pytorch-cuda              12.1                 ha16c6d3_5    pytorch
pytorch-mutex             1.0                        cuda    pytorch
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1                    pypi_0    pypi
rdkit                     2023.03.3        py39hce5ca95_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.34.0                   pypi_0    pypi
reportlab                 4.1.0            py39hd1e30aa_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rlpycairo                 0.2.0              pyhd8ed1ab_0    conda-forge
rpds-py                   0.18.0                   pypi_0    pypi
scikit-learn              1.4.2                    pypi_0    pypi
scipy                     1.13.0                   pypi_0    pypi
semantic-version          2.10.0                   pypi_0    pypi
setuptools                69.5.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sleef                     3.5.1                h9b69904_2    conda-forge
sniffio                   1.3.1                    pypi_0    pypi
sqlalchemy                2.0.29           py39hd1e30aa_0    conda-forge
starlette                 0.37.2                   pypi_0    pypi
sympy                     1.12            pypyh9d50eac_103    conda-forge
threadpoolctl             3.4.0                    pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
toolz                     0.12.1                   pypi_0    pypi
torch-cluster             1.6.3                    pypi_0    pypi
torch-geometric           2.5.2                    pypi_0    pypi
torch-scatter             2.1.2+pt21cu121          pypi_0    pypi
torch-sparse              0.6.18+pt21cu121          pypi_0    pypi
torch-spline-conv         1.2.2+pt21cu121          pypi_0    pypi
torchaudio                2.1.2                py39_cu121    pytorch
torchvision               0.16.2               py39_cu121    pytorch
tqdm                      4.66.2                   pypi_0    pypi
typing-extensions         4.11.0               hd8ed1ab_0    conda-forge
typing_extensions         4.11.0             pyha770c72_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
unicodedata2              15.1.0           py39hd1e30aa_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
uvicorn                   0.29.0                   pypi_0    pypi
websockets                11.0.3                   pypi_0    pypi
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.4                h0b41bf4_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yarl                      1.9.4                    pypi_0    pypi
zipp                      3.18.1                   pypi_0    pypi
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

OS information:

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Tue_Feb__7_19:32:13_PST_2023
Cuda compilation tools, release 12.1, V12.1.66
Build cuda_12.1.r12.1/compiler.32415258_0
Python 3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:33:10) 
[GCC 12.3.0] on linux

Please help me to solve it. Thank you.

mainguyenanhvu commented 4 months ago

I found the solution here.