awfderry
commented
1 year ago This issue is caused by incompatibilities of PyG dependencies with Pytorch, and Cuda versions. It seems to be more common with older versions, so I updated the install scripts to the latest versions of all dependencies. Hopefully this makes installation less painful in the future
Hi, I prepared the environment with install_dependencies_cpu.sh in the Linux server. I found that the torch geometric could not be found, even though it was uninstalled and reinstalled.
the log is here:
(collapse) liuhongbin@slurm-master:~/soft/Pockets/COLLAPSE-main$ python search_site.py data/examples/1a0h.pdb B H363 data/datasets/pdb_embeddings.pkl --cutoff 1e-3 --verbose --num_iter 3 torch geometric not found, GNN examples will not work until it is. Traceback (most recent call last): File "search_site.py", line 8, in
from collapse import atom_info, initialize_model, process_pdb, embed_residue
File "/home/liuhongbin/soft/Pockets/COLLAPSE-main/collapse/init.py", line 1, in
from .data import process_pdb, initialize_model, embed_protein, embed_residue, embed_pocket
File "/home/liuhongbin/soft/Pockets/COLLAPSE-main/collapse/data.py", line 21, in
from torch_geometric.data import Batch
File "/home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/site-packages/torch_geometric/init.py", line 2, in
import torch_geometric.nn
File "/home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/site-packages/torch_geometric/nn/init.py", line 2, in
from .data_parallel import DataParallel
File "/home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/site-packages/torch_geometric/nn/data_parallel.py", line 5, in
from torch_geometric.data import Batch
File "/home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/site-packages/torch_geometric/data/init.py", line 1, in
from .data import Data
File "/home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/site-packages/torch_geometric/data/data.py", line 7, in
from torch_sparse import coalesce
File "/home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/site-packages/torch_sparse/init.py", line 18, in
torch.ops.load_library(spec.origin)
File "/home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/site-packages/torch/_ops.py", line 220, in load_library
ctypes.CDLL(path)
File "/home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/ctypes/init.py", line 373, in init
self._handle = _dlopen(self._name, mode)
OSError: /home/liuhongbin/anaconda3/envs/collapse/lib/python3.8/site-packages/torch_sparse/_version_cpu.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE