torch_geometric version incompatibilty

[tuhinraut]

I am most l;ikely facing a version incompatibility for the torch-geometric package, I tried with some older and newer versions of this package but it seems to not work with any. Could anybody help me out with their conda list of all of the packages for using DynamicBind?

/home/mili_123/DynamicBind/run_single_protein_inference.py /home/mili_123/DynamicBind
100%|█████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 40.92it/s]
hub dir /home/mili_123/DynamicBind/esm_models
Read data/prepared_for_esm_test.fasta with 1 sequences
Processing 1 of 1 batches (1 sequences)
Traceback (most recent call last):
File "/home/mili_123/DynamicBind/inference.py", line 27, in
from torch_geometric.loader import DataLoader
File "/home/mili_123/miniconda3/envs/dynamicbind/lib/python3.10/site-packages/torch_geometric/init.py", line 1, in
import torch_geometric.utils
File "/home/mili_123/miniconda3/envs/dynamicbind/lib/python3.10/site-packages/torch_geometric/utils/init.py", line 8, in
from .dropout import dropout_adj, dropout_node, dropout_edge, dropout_path
File "/home/mili_123/miniconda3/envs/dynamicbind/lib/python3.10/site-packages/torch_geometric/utils/dropout.py", line 6, in
import torch_cluster # noqa
File "/home/mili_123/miniconda3/envs/dynamicbind/lib/python3.10/site-packages/torch_cluster/init.py", line 18, in
torch.ops.load_library(spec.origin)
File "/home/mili_123/miniconda3/envs/dynamicbind/lib/python3.10/site-packages/torch/_ops.py", line 643, in load_library
ctypes.CDLL(path)
File "/home/mili_123/miniconda3/envs/dynamicbind/lib/python3.10/ctypes/init.py", line 374, in init
self._handle = _dlopen(self._name, mode)
OSError: libcudart.so.11.0: cannot open shared object file: No such file or directory
inference complete.
Traceback (most recent call last):
File "/home/mili_123/DynamicBind/relax_final.py", line 505, in
results_path_containments = sorted(os.listdir(args.results_path))
FileNotFoundError: [Errno 2] No such file or directory: 'results/test'
final step structure relax complete.

Name Version Build Channel

biopython 1.85 pypi_0 pypi
cuda-cudart 11.7.99 0 nvidia
cuda-cupti 11.7.101 0 nvidia
cuda-libraries 11.7.1 0 nvidia
cuda-nvrtc 11.7.99 0 nvidia
cuda-nvtx 11.7.91 0 nvidia
cuda-runtime 11.7.1 0 nvidia
cuda-version 12.9 3 nvidia
numpy 1.26.4 py310h5f9d8c6_0
numpy-base 1.26.4 py310hb5e798b_0
pandas 2.3.1 py310h0158d43_0 conda-forge
pillow 11.1.0 py310hac6e08b_1
pip 25.1 pyhc872135_2
pthread-stubs 0.3 h0ce48e5_1
pycairo 1.27.0 py310h25ff670_0 conda-forge
pycparser 2.21 pyhd3eb1b0_0
pyg 2.5.2 py310_torch_2.0.0_cu117 pyg
pyg-lib 0.4.0+pt20cu117 pypi_0 pypi
pyparsing 3.2.3 pyhe01879c_2 conda-forge
pysocks 1.7.1 py310h06a4308_0
python 3.10.14 hd12c33a_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 8_cp310 conda-forge
pytorch 2.0.0 py3.10_cpu_0 pytorch
pytorch-cuda 11.7 h778d358_5 pytorch
pytorch-mutex 1.0 cpu pytorch
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py310h5eee18b_0
rdkit 2024.03.6 py310hf76b54c_0 conda-forge
scikit-learn 1.7.1 py310hc74f9fe_0
scipy 1.15.3 py310h525edd1_0
sympy 1.13.1 pypi_0 pypi
tbb 2021.8.0 hdb19cb5_0
threadpoolctl 3.5.0 py310h2f386ee_0
torch-cluster 1.6.3+pt20cu117 pypi_0 pypi
torch-geometric 2.6.1 pypi_0 pypi
torch-scatter 2.1.2+pt20cu117 pypi_0 pypi
torch-sparse 0.6.18+pt20cu117 pypi_0 pypi
torch-spline-conv 1.2.2+pt20cu117 pypi_0 pypi
torchaudio 2.0.0 py310_cpu pytorch
torchvision 0.15.0 py310_cpu pytorch
tqdm 4.67.1 py310h2f386ee_0