import error

[yuntwang]

Hi，when i import STAligner，error:

$python Python 3.8.18 (default, Sep 11 2023, 13:40:15) [GCC 11.2.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.

import STAligner terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted

why?

[zhoux85]

Hi. Are the package Pytorch and PyG correctly installed? Please check them first.

[yuntwang]

HI, these two modules have been successfully installed.

conda install -c pytorch pytorch Retrieving notices: ...working... done Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(556): Using . with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1., but conda is ignoring the .* and treating it as 1.7.1 done Solving environment: done

All requested packages already installed.

conda install -c pyg pyg Collecting package metadata (current_repodata.json): | WARNING conda.models.version:get_matcher(556): Using . with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1., but conda is ignoring the .* and treating it as 1.7.1 done Solving environment: done

All requested packages already installed.

But when loading the STAligner module, the same problem still exists：

Python 3.8.18 (default, Sep 11 2023, 13:40:15) 
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import STAligner
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted

[zhoux85]

Can you 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

[yuntwang]

`$python Python 3.8.18 (default, Sep 11 2023, 13:40:15) [GCC 11.2.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.

import torch from torch_geometric.data import Data terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted `

[yuntwang]

Reinstalled the following module

torch==1.9.1
torch-geometric==2.0.3
torch-cluster==1.5.9
torch-scatter==2.0.9
torch-sparse==0.6.12

Recall module

import Python 3.8.18 (default, Sep 11 2023, 13:40:15) 
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
 import STAligner
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/share/nas1/wangyt/software/STAligner-master/STAligner/__init__.py", line 13, in <module>
    from .train_STAligner import train_STAligner, train_STAligner_subgraph
  File "/share/nas1/wangyt/software/STAligner-master/STAligner/train_STAligner.py", line 7, in <module>
    from .STALIGNER import STAligner
  File "/share/nas1/wangyt/software/STAligner-master/STAligner/STALIGNER.py", line 9, in <module>
    from .gat_conv import GATConv
  File "/share/nas1/wangyt/software/STAligner-master/STAligner/gat_conv.py", line 2, in <module>
    from torch_geometric.typing import (OptPairTensor, Adj, Size, NoneType,
  File "/share/nas1/wangyt/software/miniconda3/envs/STAligner/lib/python3.8/site-packages/torch_geometric/__init__.py", line 4, in <module>
    import torch_geometric.data
  File "/share/nas1/wangyt/software/miniconda3/envs/STAligner/lib/python3.8/site-packages/torch_geometric/data/__init__.py", line 1, in <module>
    from .data import Data
  File "/share/nas1/wangyt/software/miniconda3/envs/STAligner/lib/python3.8/site-packages/torch_geometric/data/data.py", line 9, in <module>
    from torch_sparse import SparseTensor
  File "/share/nas1/wangyt/software/miniconda3/envs/STAligner/lib/python3.8/site-packages/torch_sparse/__init__.py", line 19, in <module>
    torch.ops.load_library(spec.origin)
  File "/share/nas1/wangyt/software/miniconda3/envs/STAligner/lib/python3.8/site-packages/torch/_ops.py", line 104, in load_library
    ctypes.CDLL(path)
  File "/share/nas1/wangyt/software/miniconda3/envs/STAligner/lib/python3.8/ctypes/__init__.py", line 373, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: libtorch_cuda_cu.so: cannot open shared object file: No such file or directory

My server does not have a GPU……

[zhoux85]

Both torch and pyg have CPU version. If your server dose not have GPU, please install the CPU version. In my experience, CPU version may be easier to be installed.