RoseTTAFold
RoseTTAFold copied to clipboard
Published
20 hours ago •
RosettaCommons
RosettaCommons
OSError: libtorch_cuda_cu.so: cannot open shared object file: No such file or directory
Hi, thank you very much for this awesome work!
I tried to do complex modeling, but I encountered the following error.
$ python network/predict_complex.py -i example/complex_modeling/filtered2.a3m -o complex -Ls 218 310
Using backend: pytorch
Traceback (most recent call last):
File "network/predict_complex.py", line 8, in <module>
from RoseTTAFoldModel import RoseTTAFoldModule_e2e
File "/home/shengfa/RoseTTAFold/network/RoseTTAFoldModel.py", line 4, in <module>
from Attention_module_w_str import IterativeFeatureExtractor
File "/home/shengfa/RoseTTAFold/network/Attention_module_w_str.py", line 9, in <module>
from InitStrGenerator import InitStr_Network
File "/home/shengfa/RoseTTAFold/network/InitStrGenerator.py", line 6, in <module>
import torch_geometric
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_geometric/__init__.py", line 5, in <module>
import torch_geometric.data
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_geometric/data/__init__.py", line 1, in <module>
from .data import Data
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_geometric/data/data.py", line 8, in <module>
from torch_sparse import coalesce, SparseTensor
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_sparse/__init__.py", line 14, in <module>
torch.ops.load_library(importlib.machinery.PathFinder().find_spec(
File "/home/shengfa/.local/lib/python3.8/site-packages/torch/_ops.py", line 105, in load_library
ctypes.CDLL(path)
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/ctypes/__init__.py", line 381, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libtorch_cuda_cu.so: cannot open shared object file: No such file or directory
I have installed the environment using the below script:
# If your NVIDIA driver compatible with cuda11
conda env create -f RoseTTAFold-linux.yml
And the drivers are as follows:
$ nvidia-smi
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 455.23.05 Driver Version: 455.23.05 CUDA Version: 11.1 |
|-------------------------------+----------------------+----------------------+
$ conda list
# packages in environment at /home/shengfa/anaconda3/envs/RoseTTAFold:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main conda-forge
_openmp_mutex 4.5 1_gnu
biopython 1.78 py38h497a2fe_2 conda-forge
blas 1.0 mkl conda-forge
blast-legacy 2.2.26 2 biocore
brotlipy 0.7.0 py38h497a2fe_1001 conda-forge
bzip2 1.0.8 h7b6447c_0
ca-certificates 2021.5.25 h06a4308_1
certifi 2021.5.30 py38h06a4308_0
cffi 1.14.5 py38ha65f79e_0 conda-forge
chardet 3.0.4 pypi_0 pypi
cryptography 3.4.7 py38ha5dfef3_0 conda-forge
cudatoolkit 11.1.74 h6bb024c_0 nvidia
decorator 4.4.2 pypi_0 pypi
dgl-cu110 0.6.1 pypi_0 pypi
ffmpeg 4.3 hf484d3e_0 pytorch
freetype 2.10.4 h5ab3b9f_0
gmp 6.2.1 h2531618_2
gnutls 3.6.15 he1e5248_0
googledrivedownloader 0.4 pyhd3deb0d_1 conda-forge
hhsuite 3.3.0 py38pl5262hc37a69a_2 bioconda
idna 2.10 pyh9f0ad1d_0 conda-forge
intel-openmp 2021.2.0 h06a4308_610
jinja2 3.0.1 pyhd8ed1ab_0 conda-forge
joblib 1.0.1 pyhd8ed1ab_0 conda-forge
jpeg 9b h024ee3a_2
lame 3.100 h7b6447c_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.35.1 h7274673_9
libblas 3.9.0 9_mkl conda-forge
libcblas 3.9.0 9_mkl conda-forge
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgfortran-ng 7.5.0 h14aa051_19 conda-forge
libgfortran4 7.5.0 h14aa051_19 conda-forge
libgomp 9.3.0 h5101ec6_17
libiconv 1.15 h63c8f33_5
libidn2 2.3.1 h27cfd23_0
liblapack 3.9.0 9_mkl conda-forge
libpng 1.6.37 hbc83047_0
libstdcxx-ng 9.3.0 hd4cf53a_17
libtasn1 4.16.0 h27cfd23_0
libtiff 4.2.0 h85742a9_0
libunistring 0.9.10 h27cfd23_0
libuv 1.40.0 h7b6447c_0
libwebp-base 1.2.0 h27cfd23_0
lie-learn 0.0.1.post1 pypi_0 pypi
lz4-c 1.9.3 h2531618_0
markupsafe 2.0.1 py38h497a2fe_0 conda-forge
mkl 2021.2.0 h06a4308_296
mkl-service 2.3.0 py38h27cfd23_1
mkl_fft 1.3.0 py38h42c9631_2
mkl_random 1.2.1 py38ha9443f7_2
ncurses 6.2 he6710b0_1
nettle 3.7.3 hbbd107a_1
networkx 2.5 py_0 conda-forge
ninja 1.10.2 hff7bd54_1
numpy 1.20.2 py38h2d18471_0
numpy-base 1.20.2 py38hfae3a4d_0
olefile 0.46 py_0 conda-forge
openh264 2.1.0 hd408876_0
openssl 1.1.1k h27cfd23_0
packaging 20.9 pyhd3eb1b0_0
pandas 1.2.5 py38h1abd341_0 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
pillow 8.2.0 py38he98fc37_0
pip 21.1.3 py38h06a4308_0
psipred 4.01 1 biocore
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyrosetta 2021.29+release.d8f55669792 pypi_0 pypi
pysocks 1.7.1 py38h578d9bd_3 conda-forge
python 3.8.10 h12debd9_8
python-dateutil 2.8.1 py_0 conda-forge
python-louvain 0.15 pyhd3deb0d_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytorch 1.9.0 py3.8_cuda11.1_cudnn8.0.5_0 pytorch
pytorch-cluster 1.5.9 py38_torch_1.9.0_cu111 rusty1s
pytorch-geometric 1.7.2 py38_torch_1.9.0_cu111 rusty1s
pytorch-scatter 2.0.7 py38_torch_1.9.0_cu111 rusty1s
pytorch-sparse 0.6.10 py38_torch_1.9.0_cu111 rusty1s
pytorch-spline-conv 1.2.1 py38_torch_1.9.0_cu111 rusty1s
pytz 2021.1 pyhd8ed1ab_0 conda-forge
readline 8.1 h27cfd23_0
requests 2.25.1 pyhd3deb0d_0 conda-forge
scikit-learn 0.24.2 py38ha9443f7_0
scipy 1.7.0 pypi_0 pypi
setuptools 52.0.0 py38h06a4308_0
six 1.16.0 pyhd3eb1b0_0
sqlite 3.36.0 hc218d9a_0
threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge
tk 8.6.10 hbc83047_0
torchaudio 0.9.0 py38 pytorch
torchvision 0.10.0 py38_cu111 pytorch
tqdm 4.61.1 pyhd8ed1ab_0 conda-forge
typing_extensions 3.10.0.0 pyh06a4308_0
urllib3 1.25.11 pypi_0 pypi
wheel 0.36.2 pyhd3eb1b0_0
xz 5.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.9 haebb681_0
How can I fix this error? Thank you for any help you can offer.
I also encountered this problem. It may be caused by the mismatch between the CUDA version and the pytoch version. First uninstall pytoch, and then reinstall the pytoch that conforms to your CUDA version, and then succeeded. Refer to the following articles: http://www.zzvips.com/article/193757.html
