pytorch_geometric: Undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

📚 Installation

Environment

  • OS:18.4
  • Python version: 3.6
  • PyTorch version:1.4
  • CUDA/cuDNN version:10.0
  • GCC version:7.4
  • How did you try to install PyTorch Geometric and its extensions (pip, source): pip wheel
  • Any other relevant information:

_libgcc_mutex 0.1 main
_pytorch_select 0.2 gpu_0
blas 1.0 mkl
ca-certificates 2020.1.1 0
certifi 2019.11.28 py36_1
cffi 1.14.0 py36h2e261b9_0
chardet 3.0.4 pypi_0 pypi cudatoolkit 10.0.130 0
cudnn 7.6.5 cuda10.0_0
cycler 0.10.0 pypi_0 pypi decorator 4.4.2 pypi_0 pypi freetype 2.9.1 h8a8886c_1
googledrivedownloader 0.4 pypi_0 pypi h5py 2.10.0 pypi_0 pypi idna 2.9 pypi_0 pypi imageio 2.8.0 pypi_0 pypi intel-openmp 2020.0 166
isodate 0.6.0 pypi_0 pypi joblib 0.14.1 pypi_0 pypi jpeg 9b h024ee3a_2
kiwisolver 1.1.0 pypi_0 pypi ld_impl_linux-64 2.33.1 h53a641e_7
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
libpng 1.6.37 hbc83047_0
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.1.0 h2733197_0
llvmlite 0.31.0 pypi_0 pypi matplotlib 3.2.1 pypi_0 pypi mkl 2020.0 166
mkl-service 2.3.0 py36he904b0f_0
mkl_fft 1.0.15 py36ha843d7b_0
mkl_random 1.1.0 py36hd6b4f25_0
ncurses 6.2 he6710b0_0
networkx 2.4 pypi_0 pypi ninja 1.9.0 py36hfd86e86_0
numba 0.48.0 pypi_0 pypi numpy 1.18.1 py36h4f9e942_0
numpy-base 1.18.1 py36hde5b4d6_1
olefile 0.46 py36_0
openssl 1.1.1e h7b6447c_0
pandas 1.0.3 pypi_0 pypi pillow 7.0.0 py36hb39fc2d_0
pip 20.0.2 py36_1
plyfile 0.7.2 pypi_0 pypi pycparser 2.20 py_0
pyparsing 2.4.6 pypi_0 pypi python 3.6.10 hcf32534_1
python-dateutil 2.8.1 pypi_0 pypi pytorch 1.4.0 cuda100py36h75a84eb_0
pytz 2019.3 pypi_0 pypi pywavelets 1.1.1 pypi_0 pypi rdflib 4.2.2 pypi_0 pypi readline 8.0 h7b6447c_0
requests 2.23.0 pypi_0 pypi scikit-image 0.16.2 pypi_0 pypi scikit-learn 0.22.2.post1 pypi_0 pypi scipy 1.4.1 pypi_0 pypi setuptools 46.1.1 py36_0
six 1.14.0 py36_0
sqlite 3.31.1 h7b6447c_0
tk 8.6.8 hbc83047_0
torch-cluster 1.5.3 pypi_0 pypi torch-geometric 1.4.3 pypi_0 pypi torch-scatter 2.0.4 pypi_0 pypi torch-sparse 0.6.1 pypi_0 pypi torch-spline-conv 1.2.0 pypi_0 pypi torchvision 0.2.1 py36_0
urllib3 1.25.8 pypi_0 pypi wheel 0.34.2 py36_0
xz 5.2.4 h14c3975_4
zlib 1.2.11 h7b6447c_3
zstd 1.3.7 h0b5b093_0

Checklist

  • I followed the installation guide.
  • I cannot find my error message in the FAQ.
  • [ 1 ] I set up CUDA correctly and can compile CUDA code via nvcc.
  • I have cloned the repository and tried a manual installation from source.
  • I do have multiple CUDA versions on my machine.
  • I checked if the official extension example runs on my machine.
  • The offical extension example runs on my machine.

Additional context

my problem like https://github.com/rusty1s/pytorch_geometric/issues/999

File “main.py”, line 2, in <module> from torch_geometric.datasets import TUDataset File “/home/xiejunlin/anaconda3/envs/graph/lib/python3.6/site-packages/torch_geometric/init.py”, line 2, in <module> import torch_geometric.nn File “/home/xiejunlin/anaconda3/envs/graph/lib/python3.6/site-packages/torch_geometric/nn/init.py”, line 2, in <module> from .data_parallel import DataParallel File “/home/xiejunlin/anaconda3/envs/graph/lib/python3.6/site-packages/torch_geometric/nn/data_parallel.py”, line 5, in <module> from torch_geometric.data import Batch File “/home/xiejunlin/anaconda3/envs/graph/lib/python3.6/site-packages/torch_geometric/data/init.py”, line 1, in <module> from .data import Data File “/home/xiejunlin/anaconda3/envs/graph/lib/python3.6/site-packages/torch_geometric/data/data.py”, line 7, in <module> from torch_sparse import coalesce File “/home/xiejunlin/anaconda3/envs/graph/lib/python3.6/site-packages/torch_sparse/init.py”, line 23, in <module> raise OSError(e) OSError: /home/xiejunlin/anaconda3/envs/graph/lib/python3.6/site-packages/torch_sparse/_version.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

can you have any idea?

About this issue

  • Original URL
  • State: closed
  • Created 4 years ago
  • Comments: 15 (2 by maintainers)

Most upvoted comments

I encounter this problem too. The installation of “pytorch_geometric” is a terrible, awful, and horrible experience ever!!!

+58
dongwei156 on Mar 30, 2020

I have solved this problem. The reason is that: do not install pytorch via anaconda-navigator ! It will install both cpu and gpu versions, even though you only select the pytorch. You can download the specific version of the pytorch from:

https://download.pytorch.org/whl/torch_stable.html,

and this problem will be solved. All dependent packages are listed: cu101/torch-1.4.0-cp38-cp38-linux_x86_64.whl cu101/torchvision-0.5.0-cp38-cp38-linux_x86_64.whl torch_cluster-1.5.3+cu101-cp38-cp38-linux_x86_64.whl torch_scatter-2.0.4+cu101-cp38-cp38-linux_x86_64.whl torch_sparse-0.6.1+cu101-cp38-cp38-linux_x86_64.whl torch_spline_conv-1.2.0+cu101-cp38-cp38-linux_x86_64.whl

The author is right! Multi-versions of pytorch (cpu and gpu) result in this problem! I am sorry about my comments in yesterday. Pytorch geometric is an excellent project !!!

+5
dongwei156 on Mar 31, 2020

好吧，我已经在多个平台上测试了所有车轮，并且它们都运行良好，所以我不知道到底是什么问题。邀请您深入研究此问题，并找出为什么PyTorch无法_version.so在您的OS上加载。 此外，请注意，您无需使用轮子，可以始终从源代码安装。

我已经解决了这个问题。原因是：不要通过anaconda-navigator安装pytorch！即使您仅选择pytorch，它也会安装cpu和gpu版本。您可以从以下位置下载特定版本的pytorch： https://download.pytorch.org/whl/torch_stable.html， 并且这个问题将得到解决。列出了所有相关软件包： cu101 / torch-1.4.0-cp38-cp38-linux_x86_64.whl cu101 / torchvision-0.5.0-cp38-cp38-linux_x86_64.whl torch_cluster-1.5.3 + cu101-cp38-cp38-cp38-linux_x86_64。 whl torch_scatter-2.0.4 + cu101-cp38-cp38-linux_x86_64.whl torch_sparse-0.6.1 + cu101-cp38-cp38-linux_x86_64.whl torch_spline_conv-1.2.0 + cu101-cp38-cp38-linux_x86_64.whl 你是对的！pytorch的多版本（cpu和gpu）导致此问题！我对昨天的评论感到抱歉。Pytorch Geometric是一个出色的项目！

So we are newer ~~~ But I think if you have a friend who have installed it , you can ask him to copy the environment to you.Because it is faster … Anyway ,thanks~~~~~~🙂

This thread pops up on when googling the error. Just going to add my solution for this with the latest conda formula. I had to remove torch via pip and reinstall it.

conda create -n pyg
conda activate pyg
conda install pyg -c pyg -c conda-forge
pip uninstall torch
pip install torch torchvision torchaudio
+4
keshavd on Nov 24, 2021
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