installation problems

[Srivathsan-Srinivas]

I have a 3.11.5 virtual-env (using pyenv). It looks like I already have pyg-lib and torc-sparse. But, while running PyG code, I get the classic error ImportError: 'NeighborSampler' requires either 'pyg-lib' or 'torch-sparse'. Below are some installation details of my machine (M1 Mac, Sonoma 14.6.1). Any help is appreciated.

(ve_3.11.5) Sri@Harnis-MBP ~ % python3 -m pip install pyg-lib torch-sparse -f https://pytorch-geometric.com/whl/torch-2.5.1+cpu.html
Looking in links: https://pytorch-geometric.com/whl/torch-2.5.1+cpu.html
Requirement already satisfied: pyg-lib in ./.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages (0.4.0+pt23)
Requirement already satisfied: torch-sparse in ./.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages (0.6.18)
Requirement already satisfied: scipy in ./.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages (from torch-sparse) (1.14.1)
Requirement already satisfied: numpy<2.3,>=1.23.5 in ./.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages (from scipy->torch-sparse) (1.26.4)
(ve_3.11.5) Sri@Harnis-MBP ~ %

(ve_3.11.5) Sri@Harnis-MBP graphs % python
Python 3.11.5 (main, Nov  4 2024, 12:49:21) [Clang 15.0.0 (clang-1500.3.9.4)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> import torch_geometric
/Users/Sri/.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: dlopen(/Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/libpyg.so, 0x0006): Library not loaded: /Library/Frameworks/Python.framework/Versions/3.11/Python
  Referenced from: <75FFC412-93B5-322B-8E6D-268DA3498CF4> /Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/libpyg.so
  Reason: tried: '/Library/Frameworks/Python.framework/Versions/3.11/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/Python.framework/Versions/3.11/Python' (no such file), '/Library/Frameworks/Python.framework/Versions/3.11/Python' (no such file)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/Users/Sri/.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: dlopen(/Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/torch_sparse/_version_cpu.so, 0x0006): Symbol not found: __ZN5torch3jit17parseSchemaOrNameERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
  Referenced from: <C09D3DBC-DF97-3764-B860-5AF64666FD35> /Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/torch_sparse/_version_cpu.so
  Expected in:     <A51C8C05-245A-3989-8D3C-9A6704422CA5> /Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/torch/lib/libtorch_cpu.dylib
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
>>> 

The strange thing is that I do not see "/Library/Frameworks/Python.framework/"

(ve_3.11.5) Sri@Harnis-MBP ~ % cd /Library/Frameworks
Sri@Harnis-MBP Frameworks % ls -l
total 0
drwxr-xr-x  6 root  wheel  192 Aug  4 05:31 CoreRepairCore.framework
drwxr-xr-x  5 root  wheel  160 Aug  4 05:31 CoreRepairKit.framework
lrwxr-xr-x@ 1 root  wheel   50 Aug  4 05:31 iTunesLibrary.framework -> /System/Library/Frameworks/iTunesLibrary.framework
Sri@Harnis-MBP Frameworks %

(ve_3.11.5) Sri@Harnis-MBP ~ % which python
/Users/Sri/.pyenv/shims/python
(ve_3.11.5) Sri@Harnis-MBP ~ % python -V
Python 3.11.5
(ve_3.11.5) Sri@Harnis-MBP ~ %

When I run a basic PyG code, I get ImportError: 'NeighborSampler' requires either 'pyg-lib' or 'torch-sparse'.

>>> import pyg_lib
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/Sri/.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages/pyg_lib/__init__.py", line 39, in <module>
    load_library('libpyg')
  File "/Users/Sri/.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages/pyg_lib/__init__.py", line 36, in load_library
    torch.ops.load_library(spec.origin)
  File "/Users/Sri/.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages/torch/_ops.py", line 1350, in load_library
    ctypes.CDLL(path)
  File "/Users/Sri/.pyenv/versions/3.11.5/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(/Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/libpyg.so, 0x0006): Library not loaded: /Library/Frameworks/Python.framework/Versions/3.11/Python
  Referenced from: <75FFC412-93B5-322B-8E6D-268DA3498CF4> /Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/libpyg.so
  Reason: tried: '/Library/Frameworks/Python.framework/Versions/3.11/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/Python.framework/Versions/3.11/Python' (no such file), '/Library/Frameworks/Python.framework/Versions/3.11/Python' (no such file)
  
  
>>> import torch_sparse
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/Sri/.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages/torch_sparse/__init__.py", line 18, in <module>
    torch.ops.load_library(spec.origin)
  File "/Users/Sri/.pyenv/versions/ve_3.11.5/lib/python3.11/site-packages/torch/_ops.py", line 1350, in load_library
    ctypes.CDLL(path)
  File "/Users/Sri/.pyenv/versions/3.11.5/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(/Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/torch_sparse/_version_cpu.so, 0x0006): Symbol not found: __ZN5torch3jit17parseSchemaOrNameERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
  Referenced from: <C09D3DBC-DF97-3764-B860-5AF64666FD35> /Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/torch_sparse/_version_cpu.so
  Expected in:     <A51C8C05-245A-3989-8D3C-9A6704422CA5> /Users/Sri/.pyenv/versions/3.11.5/envs/ve_3.11.5/lib/python3.11/site-packages/torch/lib/libtorch_cpu.dylib
>>> 

[Srivathsan-Srinivas]

I fixed this issue by installing python by brew install python.