Open xyang2316 opened 2 years ago
How did you install PyTorch in the first place? Are you using the official version from pytorch.org?
Yes, the Pytorch was installed from the official site.
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)
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!
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
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.
You may need to link the full log of
pip install --verbose torch-scatter
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
Can you show me the output of conda list
?
@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.
-- _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!
It looks like both PyG and PyTorch are installed from pip
(rather from conda
), right? What commands did you run to install them?
@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
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?
@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.
@rusty1s
Hello!!!!
I tested pytorch 1.10.0
whith cuda 10.2
,
the same as 1.4.0 ,the error did not happen!
Thanks for confirming. I hope you are good to go now.
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.
The problem is that you install the PyTorch version from conda-forge
, while you need the one from -c pytorch
.
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)
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.
I found the solution here.
😵 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
torch_geometric.__version__
): 2.0.3torch.__version__
): 1.93.9
): 3.8conda
,pip
, source): piptorch-scatter
):Additional context