torchdrug
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Published
20 hours ago •
DeepGraphLearning
DeepGraphLearning
Error installing OSError undefined symbols
Background
I am facing installation issues. Note, my installation is in a fresh conda environment, and my only manual installs were numpy and pytorch before running
conda install -c milagraph -c conda-forge torchdrug
Details below, and happy to provide more info. Thanks!
System and Conda Env Info
System information Ubuntu 20.04.2 LTS, 64-bit No GPU
python --version
> Python 3.8.8
conda --version
> conda 4.10.3
conda --list
># Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
alsa-lib 1.2.3 h516909a_0 conda-forge
boost 1.74.0 py38hc10631b_3 conda-forge
boost-cpp 1.74.0 h312852a_4 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2021.5.30 ha878542_0 conda-forge
cairo 1.16.0 h6cf1ce9_1008 conda-forge
certifi 2021.5.30 py38h578d9bd_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
cpuonly 1.0 0 pytorch
cycler 0.10.0 py_2 conda-forge
dbus 1.13.6 h48d8840_2 conda-forge
decorator 5.0.9 pyhd8ed1ab_0 conda-forge
expat 2.4.1 h9c3ff4c_0 conda-forge
fontconfig 2.13.1 hba837de_1005 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
glib 2.68.3 h9c3ff4c_0 conda-forge
glib-tools 2.68.3 h9c3ff4c_0 conda-forge
greenlet 1.1.0 py38h709712a_0 conda-forge
gst-plugins-base 1.18.4 hf529b03_2 conda-forge
gstreamer 1.18.4 h76c114f_2 conda-forge
icu 68.1 h58526e2_0 conda-forge
intel-openmp 2021.3.0 h06a4308_3350
jbig 2.1 h7f98852_2003 conda-forge
jinja2 3.0.1 pyhd8ed1ab_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
kiwisolver 1.3.1 py38h1fd1430_1 conda-forge
krb5 1.19.2 hcc1bbae_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.35.1 h7274673_9
lerc 2.2.1 h9c3ff4c_0 conda-forge
libblas 3.9.0 11_linux64_openblas conda-forge
libcblas 3.9.0 11_linux64_openblas conda-forge
libclang 11.1.0 default_ha53f305_1 conda-forge
libdeflate 1.7 h7f98852_5 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libevent 2.1.10 hcdb4288_3 conda-forge
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgfortran-ng 11.1.0 h69a702a_8 conda-forge
libgfortran5 11.1.0 h6c583b3_8 conda-forge
libglib 2.68.3 h3e27bee_0 conda-forge
libgomp 9.3.0 h5101ec6_17
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 11_linux64_openblas conda-forge
libllvm11 11.1.0 hf817b99_2 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.17 pthreads_h8fe5266_1 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 13.3 hd57d9b9_0 conda-forge
libstdcxx-ng 9.3.0 hd4cf53a_17
libtiff 4.3.0 hf544144_1 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.2.0 h7f98852_2 conda-forge
libxcb 1.13 h7f98852_1003 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
markupsafe 2.0.1 py38h497a2fe_0 conda-forge
matplotlib 3.4.2 py38h578d9bd_0 conda-forge
matplotlib-base 3.4.2 py38hcc49a3a_0 conda-forge
mkl 2021.3.0 h06a4308_520
mysql-common 8.0.25 ha770c72_2 conda-forge
mysql-libs 8.0.25 hfa10184_2 conda-forge
ncurses 6.2 he6710b0_1
networkx 2.5 py_0 conda-forge
ninja 1.10.2 h4bd325d_0 conda-forge
nspr 4.30 h9c3ff4c_0 conda-forge
nss 3.67 hb5efdd6_0 conda-forge
numpy 1.21.1 py38h9894fe3_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1k h7f98852_0 conda-forge
pandas 1.3.1 py38h1abd341_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pillow 8.3.1 py38h8e6f84c_0 conda-forge
pip 21.2.3 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycairo 1.20.1 py38hf61ee4a_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.12.3 py38h578d9bd_7 conda-forge
pyqt-impl 5.12.3 py38h7400c14_7 conda-forge
pyqt5-sip 4.19.18 py38h709712a_7 conda-forge
pyqtchart 5.12 py38h7400c14_7 conda-forge
pyqtwebengine 5.12.1 py38h7400c14_7 conda-forge
python 3.8.11 h12debd9_0_cpython
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytorch 1.4.0 py3.8_cpu_0 [cpuonly] pytorch
pytorch_scatter 2.0.4 py38h9235441_1 conda-forge
pytz 2021.1 pyhd8ed1ab_0 conda-forge
qt 5.12.9 hda022c4_4 conda-forge
rdkit 2021.03.4 py38hf8acc3d_0 conda-forge
readline 8.1 h27cfd23_0
reportlab 3.5.68 py38hadf75a6_0 conda-forge
setuptools 52.0.0 py38h06a4308_0
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlalchemy 1.4.22 py38h497a2fe_0 conda-forge
sqlite 3.36.0 hc218d9a_0
tk 8.6.10 hbc83047_0
torchaudio 0.4.0 py38 pytorch
torchdrug 0.1.0 h39ad8c7 milagraph
torchvision 0.5.0 py38_cpu [cpuonly] pytorch
tornado 6.1 py38h497a2fe_1 conda-forge
tqdm 4.62.0 pyhd8ed1ab_0 conda-forge
wheel 0.36.2 pyhd3eb1b0_0
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 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 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3
zstd 1.5.0 ha95c52a_0 conda-forge
Error output
Here is the error:
(torchdrug) 1_Projects $ python
Python 3.8.11 (default, Aug 3 2021, 15:09:35)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torchdrug
Traceback (most recent call last):
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torch_scatter/__init__.py", line 12, in <module>
torch.ops.load_library(importlib.machinery.PathFinder().find_spec(
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torch/_ops.py", line 106, in load_library
ctypes.CDLL(path)
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/ctypes/__init__.py", line 373, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torch_scatter/_version.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torchdrug/__init__.py", line 1, in <module>
from . import patch
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torchdrug/patch.py", line 12, in <module>
from torchdrug import core, data
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torchdrug/core/__init__.py", line 2, in <module>
from .engine import Engine
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torchdrug/core/engine.py", line 10, in <module>
from torchdrug import data, core, utils
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torchdrug/data/__init__.py", line 1, in <module>
from .graph import Graph, PackedGraph, cat
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torchdrug/data/graph.py", line 9, in <module>
from torch_scatter import scatter_add, scatter_min
File "/home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torch_scatter/__init__.py", line 21, in <module>
raise OSError(e)
OSError: /home/murph213/anaconda3/envs/torchdrug/lib/python3.8/site-packages/torch_scatter/_version.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE
Hi! This means torch_scatter can't load its binary properly. Maybe it's a problem for the torch_scatter from the conda-forge channel.
Could you try to add -c rusty1s before -c conda-forge? This will install torch_scatter from its official channel. If not, you may try manually install torch and torch_scatter using their recommended commands, and then install torchdrug.
I tried both suggestions and neither worked. (I got a similar error). I also tried building from source, following the instructions:
conda install -c conda-forge rdkit
git clone https://github.com/DeepGraphLearning/torchdrug
cd torchdrug
pip install -r requirements.txt
python setup.py install
I got the error
(td2) torchdrug $ python
Python 3.8.11 (default, Aug 3 2021, 15:09:35)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torchdrug
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/murph213/torchdrug/torchdrug/__init__.py", line 1, in <module>
from . import patch
File "/home/murph213/torchdrug/torchdrug/patch.py", line 12, in <module>
from torchdrug import core, data
File "/home/murph213/torchdrug/torchdrug/core/__init__.py", line 2, in <module>
from .engine import Engine
File "/home/murph213/torchdrug/torchdrug/core/engine.py", line 10, in <module>
from torchdrug import data, core, utils
File "/home/murph213/torchdrug/torchdrug/data/__init__.py", line 1, in <module>
from .graph import Graph, PackedGraph, cat
File "/home/murph213/torchdrug/torchdrug/data/graph.py", line 11, in <module>
from torchdrug import core, utils
File "/home/murph213/torchdrug/torchdrug/utils/__init__.py", line 3, in <module>
from .torch import load_extension, cpu, cuda, detach, clone, mean, cat, stack, sparse_coo_tensor
File "/home/murph213/torchdrug/torchdrug/utils/torch.py", line 4, in <module>
from torch._six import container_abcs
ImportError: cannot import name 'container_abcs' from 'torch._six' (/home/murph213/anaconda3/envs/td2/lib/python3.8/site-packages/torch/_six.py)
I am happy to try either the source or conda solution; which do you think is more stable? If conda, could you provide which instructions you think are most likely to work and we can try from there? Thank you.
Edit: for instance, maybe you can share your python version and the installation steps you followed? That would be very helpful :). I am using the CPU installation, by the way.
I thought that maybe using LTS PyTorch would help, so I tried
conda create -n torchdrug9 python=3.8
conda activate torchdrug9
conda install numpy
conda install pytorch torchvision torchaudio cpuonly -c pytorch-lts
conda install -c milagraph -c conda-forge torchdrug
but I got a different error:
>>> import torchdrug
Traceback (most recent call last):
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torch_scatter/__init__.py", line 12, in <module>
torch.ops.load_library(importlib.machinery.PathFinder().find_spec(
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torch/_ops.py", line 104, in load_library
ctypes.CDLL(path)
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/ctypes/__init__.py", line 373, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torch_scatter/_version.so: undefined symbol: _ZN3c1017RegisterOperatorsC1Ev
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torchdrug/__init__.py", line 1, in <module>
from . import patch
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torchdrug/patch.py", line 12, in <module>
from torchdrug import core, data
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torchdrug/core/__init__.py", line 2, in <module>
from .engine import Engine
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torchdrug/core/engine.py", line 10, in <module>
from torchdrug import data, core, utils
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torchdrug/data/__init__.py", line 1, in <module>
from .graph import Graph, PackedGraph, cat
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torchdrug/data/graph.py", line 9, in <module>
from torch_scatter import scatter_add, scatter_min
File "/home/murph213/anaconda3/envs/torchdrug9/lib/python3.8/site-packages/torch_scatter/__init__.py", line 18, in <module>
raise RuntimeError(
RuntimeError: Expected PyTorch version 1.4 but found version 1.8
Similarly for
conda install -c milagraph -c rusty1s -c conda-forge torchdrug
I finally got an installation that works. I think the key points were to be careful to use the supported version of PyTorch, install the correct torch-scatter for that PyTorch version, and to build from source using pip (within conda). Below are my steps for my CPU install.
conda create -n td_test python=3.8
pip3 install torch==1.8.1+cpu torchvision==0.9.1+cpu torchaudio==0.8.1 -f https://download.pytorch.org/whl/lts/1.8/torch_lts.html
# From https://github.com/rusty1s/pytorch_scatter
pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.8.0+cpu.html
conda install -c conda-forge rdkit
mkdir ~/torch_drug_test
git clone https://github.com/DeepGraphLearning/torchdrug
cd torchdrug
Then, istall the other packages in requirements.txt (but torch and torch-scatter are already installed). Next,
python setup.py install
Also, this happened to make it hard to use Jupyter Lab, so I followed these steps:
conda install -c conda-forge jupyterlab
conda install ipykernel
ipython kernel install --user
from https://stackoverflow.com/questions/53004311/how-to-add-conda-environment-to-jupyter-lab
I finally got an installation that works. I think the key points were to be careful to use the supported version of PyTorch, install the correct torch-scatter for that PyTorch version, and to build from source using pip (within conda). Below are my steps for my CPU install.
conda create -n td_test python=3.8 pip3 install torch==1.8.1+cpu torchvision==0.9.1+cpu torchaudio==0.8.1 -f https://download.pytorch.org/whl/lts/1.8/torch_lts.html # From https://github.com/rusty1s/pytorch_scatter pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.8.0+cpu.html conda install -c conda-forge rdkit mkdir ~/torch_drug_test git clone https://github.com/DeepGraphLearning/torchdrug cd torchdrugThen, istall the other packages in requirements.txt (but torch and torch-scatter are already installed). Next,
python setup.py installAlso, this happened to make it hard to use Jupyter Lab, so I followed these steps:
conda install -c conda-forge jupyterlab conda install ipykernel ipython kernel install --userfrom https://stackoverflow.com/questions/53004311/how-to-add-conda-environment-to-jupyter-lab
Thank u
