Supporting the GLIBC under 2.27

[songsong0425]

Hi. Thank you for your continued efforts in maintaining and improving the PyG library.
I’m reaching out to inquire whether there are any plans to provide pyg-lib updates compatible with environments using a GLIBC version lower than 2.27.
For reference, here are the specifications of my current environment:

• OS: Linux
• GLIBC: 2.17
• PyG: 2.6.1
• CUDA: 12.4
• Torch: 2.6
• Python: 3.9
• Corresponding wheel used: https://data.pyg.org/whl/torch-2.6.0+cu124.html

While installing pyg-lib, torch_cluster, torch_scatter, torch_sparse, and torch_spline_conv using the above wheel, I encountered runtime errors specifically with pyg-lib and torch_spline_conv due to the GLIBC version being below 2.27.
Here is a portion of the error message:

/scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /lib64/libm.so.6: version GLIBC_2.27' not found (required by /scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/libpyg.so) warnings.warn(f"An issue occurred while importing 'pyg-lib'. " /scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /lib64/libm.so.6: version GLIBC_2.27' not found (required by /scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/libpyg.so)
warnings.warn(f"An issue occurred while importing 'torch-sparse'. "

For now, I have removed pyg-lib, which allows the code to run, but I still receive the following warning:

/scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/torch_geometric/sampler/neighbor_sampler.py:61: UserWarning: Using 'NeighborSampler' without a 'pyg-lib' installation is deprecated and will be removed soon. Please install 'pyg-lib' for accelerated neighborhood sampling
warnings.warn(f"Using '{self.class.name}' without a "

To resolve this issue, would it be possible to provide updated versions of pyg-lib and torch_sparse that are compatible with environments using GLIBC versions lower than 2.27?

[akihironitta]

Hi @songsong0425, thank you for reporting the issue. We have a plan to add support for glibc 2.28+ via #457, and as far as I know, it is aligned with what PyTorch provides. However, there's no plan to add support for glibc 2.27 or its previous versions.

[akihironitta]

@songsong0425 The issue linked is no longer relevant to the discussion here, but as the error says, it seems to not be able to find torch:

  ModuleNotFoundError: No module named 'torch'
  error: subprocess-exited-with-error
  
  × Building wheel for pyg_lib (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

To address this, you need to use the command with --no-build-isolation documented in our README.md:

pip install ninja wheel
pip install --no-build-isolation git+https://github.com/pyg-team/pyg-lib.git

[songsong0425]

Thank you for your kind reply.
I tried your code, but it also returned the error message below:

(PyG_scratch1) [r902a02@glogin02 ~]$ pip install --no-build-isolation git+https://github.com/pyg-team/pyg-lib.git
Collecting git+https://github.com/pyg-team/pyg-lib.git
  Cloning https://github.com/pyg-team/pyg-lib.git to /tmp/pip-req-build-jlfj6ku5
  Running command git clone --quiet https://github.com/pyg-team/pyg-lib.git /tmp/pip-req-build-jlfj6ku5
  Resolved https://github.com/pyg-team/pyg-lib.git to commit 9f90a6d827fa970447808b7281b00f52fa9be1de
  Running command git submodule update --init --recursive -q
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: pyg-lib
  Building wheel for pyg-lib (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for pyg-lib (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [30 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-39
      creating build/lib.linux-x86_64-cpython-39/pyg_lib
      copying pyg_lib/__init__.py -> build/lib.linux-x86_64-cpython-39/pyg_lib
      copying pyg_lib/_triton.py -> build/lib.linux-x86_64-cpython-39/pyg_lib
      copying pyg_lib/home.py -> build/lib.linux-x86_64-cpython-39/pyg_lib
      copying pyg_lib/testing.py -> build/lib.linux-x86_64-cpython-39/pyg_lib
      creating build/lib.linux-x86_64-cpython-39/pyg_lib/ops
      copying pyg_lib/ops/__init__.py -> build/lib.linux-x86_64-cpython-39/pyg_lib/ops
      copying pyg_lib/ops/scatter_reduce.py -> build/lib.linux-x86_64-cpython-39/pyg_lib/ops
      creating build/lib.linux-x86_64-cpython-39/pyg_lib/partition
      copying pyg_lib/partition/__init__.py -> build/lib.linux-x86_64-cpython-39/pyg_lib/partition
      creating build/lib.linux-x86_64-cpython-39/pyg_lib/sampler
      copying pyg_lib/sampler/__init__.py -> build/lib.linux-x86_64-cpython-39/pyg_lib/sampler
      running egg_info
      creating pyg_lib.egg-info
      writing pyg_lib.egg-info/PKG-INFO
      writing dependency_links to pyg_lib.egg-info/dependency_links.txt
      writing requirements to pyg_lib.egg-info/requires.txt
      writing top-level names to pyg_lib.egg-info/top_level.txt
      writing manifest file 'pyg_lib.egg-info/SOURCES.txt'
      reading manifest file 'pyg_lib.egg-info/SOURCES.txt'
      adding license file 'LICENSE'
      adding license file 'LICENSE_radix_sort'
      writing manifest file 'pyg_lib.egg-info/SOURCES.txt'
      running build_ext
      error: [Errno 2] No such file or directory: 'cmake'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pyg-lib
Failed to build pyg-lib
ERROR: Could not build wheels for pyg-lib, which is required to install pyproject.toml-based projects

According to the last message about pyproject.toml-based projects, should I install the relevant library?
If so, I'd appreciate it if you could give any information.

[akihironitta]

Yes, running pip install cmake should make the build successful.

[akihironitta]

You could probably try pre-built nightly releases instead of building it from source:

pip install pyg-lib -f https://data.pyg.org/whl/nightly/torch-2.6.0+cu124.html

[songsong0425]

I installed the pyg-lib by installing the cmake! Hooray! Thank you!
By the way, should other libraries (e.g., torch-sparse, torch-scatter, etc.) be performed in a similar way with pyg-lib? Or follow the process in here?
When I run the pip install --verbose --no-build-isolation torch_scatter, I get a similar error.
---- (update) ----
Sorry for bothering. I installed them by pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.6.0+cu124.html.
Once again, thank you so much for your help!