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Run sample.py failed: OSError: libc10_cuda.so: cannot open shared object file: No such file or directory #22

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zyx5256 opened this issue Aug 24, 2022 · 1 comment
Open

Run sample.py failed: OSError: libc10_cuda.so: cannot open shared object file: No such file or directory #22

zyx5256 opened this issue Aug 24, 2022 · 1 comment

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@zyx5256
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zyx5256 commented Aug 24, 2022 •
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--------------------------------------------- Error Information --------------------------------------

(SBDD-3D) root@10-90-43-152:/home/jenkins/zhuyuxiao/SBDD_Project/3D-Generative-SBDD# python sample.py ./configs/sample.yml --data_id {i}
Traceback (most recent call last):
File "sample.py", line 7, in
from torch_geometric.data import Batch
File "/home/miniconda3/envs/SBDD-3D/lib/python3.8/site-packages/torch_geometric/init.py", line 4, in
import torch_geometric.data
File "/home/miniconda3/envs/SBDD-3D/lib/python3.8/site-packages/torch_geometric/data/init.py", line 1, in
from .data import Data
File "/home/miniconda3/envs/SBDD-3D/lib/python3.8/site-packages/torch_geometric/data/data.py", line 3, in
from torch_geometric.typing import OptTensor, NodeType, EdgeType
File "/home/miniconda3/envs/SBDD-3D/lib/python3.8/site-packages/torch_geometric/typing.py", line 4, in
from torch_sparse import SparseTensor
File "/home/miniconda3/envs/SBDD-3D/lib/python3.8/site-packages/torch_sparse/init.py", line 19, in
torch.ops.load_library(spec.origin)
File "/home/miniconda3/envs/SBDD-3D/lib/python3.8/site-packages/torch/_ops.py", line 110, in load_library
ctypes.CDLL(path)
File "/home/miniconda3/envs/SBDD-3D/lib/python3.8/ctypes/init.py", line 373, in init
self._handle = _dlopen(self._name, mode)
OSError: libc10_cuda.so: cannot open shared object file: No such file or directory

--------------------------------------------- My Conda Env --------------------------------------

packages in environment at /home/miniconda3/envs/SBDD-3D:

Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 1.0.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.7.4.post0 py38h497a2fe_0 conda-forge
async-timeout 3.0.1 py_1000 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
biopython 1.79 py38h497a2fe_0 conda-forge
blas 1.0 mkl conda-forge
blinker 1.4 py_1 conda-forge
boost 1.74.0 py38hc10631b_3 conda-forge
boost-cpp 1.74.0 h9359b55_0 conda-forge
brotlipy 0.7.0 py38h497a2fe_1001 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f8727e_0 defaults
ca-certificates 2022.07.19 h06a4308_0 defaults
cachetools 4.2.4 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 h3fc0475_1005 conda-forge
certifi 2022.6.15 py38h578d9bd_0 conda-forge
cffi 1.14.6 py38ha65f79e_0 conda-forge
chardet 4.0.0 py38h578d9bd_3 conda-forge
charset-normalizer 2.0.10 pyhd8ed1ab_0 conda-forge
click 8.0.3 py38h578d9bd_1 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
cpuonly 2.0 0 pytorch
cryptography 35.0.0 py38ha5dfef3_0 conda-forge
cudatoolkit 11.3.1 h2bc3f7f_2 defaults
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
decorator 4.4.2 py_0 conda-forge
easydict 1.9 py_0 conda-forge
ffmpeg 4.3 hf484d3e_0 pytorch
fontconfig 2.13.1 hba837de_1005 conda-forge
freetype 2.11.0 h70c0345_0 defaults
gettext 0.19.8.1 h0b5b191_1005 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
glib 2.69.1 h4ff587b_1 defaults
gmp 6.2.1 h58526e2_0 conda-forge
gnutls 3.6.15 he1e5248_0 defaults
google-auth 2.3.3 pyh6c4a22f_0 conda-forge
google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge
googledrivedownloader 0.4 pyhd3deb0d_1 conda-forge
grpcio 1.42.0 py38hce63b2e_0 defaults
icu 67.1 he1b5a44_0 conda-forge
idna 3.1 pyhd3deb0d_0 conda-forge
importlib-metadata 4.10.0 py38h578d9bd_0 conda-forge
intel-openmp 2021.4.0 h06a4308_3561 defaults
jinja2 3.0.3 pyhd8ed1ab_0 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
kiwisolver 1.3.1 py38h1fd1430_1 conda-forge
lame 3.100 h7f98852_1001 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 7.5.0 h14aa051_20 conda-forge
libgfortran4 7.5.0 h14aa051_20 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.15 h516909a_1006 conda-forge
libidn2 2.3.2 h7f98852_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libprotobuf 3.15.8 h780b84a_0 conda-forge
libstdcxx-ng 9.3.0 h6de172a_19 conda-forge
libtasn1 4.16.0 h27cfd23_0 defaults
libtiff 4.2.0 hbd63e13_2 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libuv 1.40.0 h7f98852_0 conda-forge
libwebp 1.2.0 h3452ae3_0 conda-forge
libwebp-base 1.2.0 h7f98852_2 conda-forge
libxcb 1.13 h7f98852_1003 conda-forge
libxml2 2.9.10 h72b56ed_2 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
markdown 3.3.6 pyhd8ed1ab_0 conda-forge
markupsafe 2.0.1 py38h497a2fe_0 conda-forge
matplotlib-base 3.3.4 py38h0efea84_0 conda-forge
mkl 2021.4.0 h06a4308_640 defaults
mkl-service 2.4.0 py38h497a2fe_0 conda-forge
mkl_fft 1.3.1 py38hd3c417c_0 defaults
mkl_random 1.2.2 py38h1abd341_0 conda-forge
multidict 5.2.0 py38h7f8727e_2 defaults
ncurses 6.3 h7f8727e_2 defaults
nettle 3.7.3 hbbd107a_1 defaults
networkx 2.5.1 pyhd8ed1ab_0 conda-forge
numpy 1.21.2 py38h20f2e39_0 defaults
numpy-base 1.21.2 py38h79a1101_0 defaults
oauthlib 3.1.1 pyhd8ed1ab_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openbabel 3.1.1 py38hf4b5c11_1 conda-forge
openh264 2.1.1 h780b84a_0 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
pandas 1.2.5 py38h1abd341_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pillow 8.4.0 py38h5aabda8_0 defaults
pip 21.2.4 pyhd8ed1ab_0 conda-forge
pixman 0.38.0 h516909a_1003 conda-forge
protobuf 3.15.8 py38h709712a_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyasn1 0.4.8 py_0 conda-forge
pyasn1-modules 0.2.7 py_0 conda-forge
pycairo 1.20.1 py38hf61ee4a_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyg 2.0.3 py38_torch_1.10.0_cpu pyg
pyjwt 2.3.0 pyhd8ed1ab_1 conda-forge
pyopenssl 21.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.6 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 py38h578d9bd_5 conda-forge
python 3.8.12 h12debd9_0 defaults
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-lmdb 0.99 py38h709712a_0 conda-forge
python-louvain 0.15 pyhd8ed1ab_1 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytorch 1.10.1 py3.8_cpu_0 pytorch
pytorch-cluster 1.5.9 py38_torch_1.10.0_cu113 pyg
pytorch-mutex 1.0 cpu pytorch
pytorch-scatter 2.0.9 py38_torch_1.10.0_cu113 pyg
pytorch-sparse 0.6.12 py38_torch_1.10.0_cu113 pyg
pytorch-spline-conv 1.2.1 py38_torch_1.10.0_cu113 pyg
pytz 2021.3 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pyyaml 5.4.1 py38h497a2fe_0 conda-forge
rdkit 2020.09.5 py38h2bca085_0 conda-forge
readline 8.1.2 h7f8727e_1 defaults
reportlab 3.5.68 py38hadf75a6_0 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.0 pyh9f0ad1d_0 conda-forge
rsa 4.8 pyhd8ed1ab_0 conda-forge
scikit-learn 1.0.2 py38h51133e4_1 defaults
scipy 1.7.3 py38hc147768_0 defaults
setuptools 58.0.4 py38h578d9bd_2 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlalchemy 1.3.23 py38h497a2fe_0 conda-forge
sqlite 3.37.0 hc218d9a_0 defaults
tensorboard 2.7.0 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.6.0 py38h2b97feb_0 conda-forge
tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.0.0 pyh8a188c0_0 conda-forge
tk 8.6.11 h21135ba_0 conda-forge
torchaudio 0.10.1 py38_cu113 pytorch
torchvision 0.11.2 py38_cu113 pytorch
tornado 6.1 py38h497a2fe_1 conda-forge
tqdm 4.62.3 pyhd8ed1ab_0 conda-forge
typing-extensions 3.10.0.2 hd8ed1ab_0 conda-forge
typing_extensions 3.10.0.2 pyha770c72_0 conda-forge
urllib3 1.26.8 pyhd8ed1ab_1 conda-forge
werkzeug 2.0.1 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
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 h516909a_1 conda-forge
yacs 0.1.6 py_0 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
yarl 1.6.3 py38h497a2fe_2 conda-forge
zipp 3.7.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.4.9 ha95c52a_0 conda-forge
@zyx5256 zyx5256 mentioned this issue Aug 24, 2022
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@luost26
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luost26 commented Aug 24, 2022

Hi,

Thank you for your interest in our work.

Can you try our latest work on SBDD? It is available at https://github.com/pengxingang/Pocket2Mol
It is based on the current work, but it is more efficient and stable.

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