Could not import torch_geometric, it says "undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs"

Question

I am trying to find a solution to the error: OSError: /opt/conda/lib/python3.7/site-packages/torch_sparse/_version_cuda.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs.

arising from the statement from torch_geometric.data import Data in Kaggle notebook.

There are solutions in github and stackoverflow, but none are working.

-- "nvcc --version" shows

"nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2020 NVIDIA Corporation Built on Wed_Jul_22_19:09:09_PDT_2020 Cuda compilation tools, release 11.0, V11.0.221 Build cuda_11.0_bu.TC445_37.28845127_0"

I tried to install torch-geometric by

1. !conda install pyg -c pyg -c conda-forge

2. !pip install pyg-lib torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.12.0+cu113.html

from here.

The first statement took more than 1 hour so I moved to the second, which installed it. But the error didn't go.

It is running with out any error in colab.

Answer 1

This issue is mentionned at https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html :

undefined symbol: make_function_schema: This issue signals (1) a version conflict between your installed PyTorch version and the ${TORCH} version specified to install the extension packages, or (2) a version conflict between the installed CUDA version of PyTorch and the ${CUDA} version specified to install the extension packages. Please verify that your PyTorch version and its CUDA version match with your installation command:

python -c "import torch; print(torch.__version__)"
python -c "import torch; print(torch.version.cuda)"
nvcc --version

For re-installation, ensure that you do not run into any caching issues by using the pip --force-reinstall --no-cache-dir flags. In addition, the pip --verbose option may help to track down any issues during installation. If you still do not find any success in installation, please try to install the extension packages from source.

So, I would try these commands, and re-install all or part of the packages into a fresh environment.

Answer 2

Looks like there could be various specific culprits to this, but in my case it was simply missing torchtext. Make sure you have that installed and the version is compatible.