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zhoux85 / STAligner

STAligner is a tool for alignment and integration of spatially resolved transcriptomics data.
MIT License
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about torch-sparse #17

Open 0225yyyyyqq opened 7 months ago

0225yyyyyqq commented 7 months ago

Traceback (most recent call last): File "T.py", line 5, in import STAligner File "/home/ya/STAligner/STAligner/init.py", line 13, in from .train_STAligner import train_STAligner, train_STAligner_subgraph File "/home/ya/STAligner/STAligner/train_STAligner.py", line 7, in from .STALIGNER import STAligner File "/home/ya/STAligner/STAligner/STALIGNER.py", line 9, in from .gat_conv import GATConv File "/home/ya/STAligner/STAligner/gat_conv.py", line 2, in from torch_geometric.typing import (OptPairTensor, Adj, Size, NoneType, File "/home/ya/anaconda3/envs/env_STAligner/lib/python3.8/site-packages/torch_geometric/init.py", line 4, in import torch_geometric.data File "/home/ya/anaconda3/envs/env_STAligner/lib/python3.8/site-packages/torch_geometric/data/init.py", line 1, in from .data import Data File "/home/ya/anaconda3/envs/env_STAligner/lib/python3.8/site-packages/torch_geometric/data/data.py", line 3, in from torch_geometric.typing import OptTensor, NodeType, EdgeType File "/home/ya/anaconda3/envs/env_STAligner/lib/python3.8/site-packages/torch_geometric/typing.py", line 4, in from torch_sparse import SparseTensor File "/home/ya/anaconda3/envs/env_STAligner/lib/python3.8/site-packages/torch_sparse/init.py", line 15, in torch.ops.load_library(importlib.machinery.PathFinder().find_spec( File "/home/ya/anaconda3/envs/env_STAligner/lib/python3.8/site-packages/torch/_ops.py", line 852, in load_library ctypes.CDLL(path) File "/home/ya/anaconda3/envs/env_STAligner/lib/python3.8/ctypes/init.py", line 373, in init self._handle = _dlopen(self._name, mode) OSError: /home/ya/anaconda3/envs/env_STAligner/lib/python3.8/site-packages/torch_sparse/_version_cpu.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

When I finished configuring the environment and tried to run it, an error like this appeared. It bothered me for a long time. I hope I can get your help. Thank you very much!

zhoux85 commented 7 months ago

Hi. It seems torch_sparse is not correctly installed. The installation of PyG is tricky, please refer the package version in https://github.com/zhoux85/STAligner/blob/master/requirement.txt

You can run the following code to test if torch and pyg are correctly installed:

import torch
from torch_geometric.data import Data
from torch_scatter import scatter_max
from torch_sparse import transpose
from torch_cluster import graclus_cluster

Hope this helps.