Some import warnings about GLIBC

[Mollyx06]

Has anyone encountered the following warning?
/opt/software/python/lib/python3.8/site-packages/torch_geometric/typing.py:54: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /lib64/libm.so.6: version GLIBC_2.27' not found (required by /opt/software/python/lib/python3.8/site-packages/libpyg.so) warnings.warn(f"An issue occurred while importing 'pyg-lib'. " /opt/software/python/lib/python3.8/site-packages/torch_geometric/typing.py:110: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /lib64/libm.so.6: version GLIBC_2.27' not found (required by /opt/software/python/lib/python3.8/site-packages/libpyg.so)
warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
It's a warning, but I'm not sure it's affecting the normal operation of my programmes

And these are the torch-related packages I successfully installed:
torch 2.3.0+cpu
torch_cluster 1.6.3+pt23cpu
torch_geometric 2.5.3
torch_scatter 2.1.2+pt23cpu
torch_sparse 0.6.18+pt23cpu
torch_spline_conv 1.2.2+pt23cpu
torchaudio 2.3.0+cpu
torchvision 0.18.0+cpu

[Mollyx06]

Added, this OS was built separately (presumably I don't have the authority to modify it), and I checked my version ldd (GNU libc) 2.17
Is there any way to get rid of the warning?

[rusty1s]

The only way to get rid of this warning is to manually install pyg-lib right now:

pip install ninja wheel cmake
pip install git+https://github.com/pyg-team/pyg-lib.git

[Mollyx06]

Thank you for your reply! But it doesn't seem to allow me to install these manually

[rusty1s]

Can you show me the full installation log when installing via

pip install --verbose git+https://github.com/pyg-team/pyg-lib.git

[songsong0425]

Hi, sorry for necroposting, but I have a similar problem with the original question.
Here's the full installation log after running pip install --verbose git+https://github.com/pyg-team/pyg-lib.git

(PyG_scratch1) [r902a02@glogin02 r902a02]$ pip install --verbose git+https://github.com/pyg-team/pyg-lib.git
Using pip 23.3 from /scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/pip (python 3.9)
Collecting git+https://github.com/pyg-team/pyg-lib.git
  Cloning https://github.com/pyg-team/pyg-lib.git to /tmp/pip-req-build-yaxg38hm
  Running command git version
  git version 1.8.3.1
  Running command git clone https://github.com/pyg-team/pyg-lib.git /tmp/pip-req-build-yaxg38hm
  Cloning into '/tmp/pip-req-build-yaxg38hm'...
  Running command git rev-parse HEAD
  35364adfb5f314a9df7aab45e1459ab4b6b50275
  Resolved https://github.com/pyg-team/pyg-lib.git to commit 35364adfb5f314a9df7aab45e1459ab4b6b50275
  Running command git submodule update --init --recursive -q
  Running command git rev-parse HEAD
  35364adfb5f314a9df7aab45e1459ab4b6b50275
  Running command pip subprocess to install build dependencies
  Collecting setuptools
    Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
  Collecting wheel
    Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
  Installing collected packages: wheel, setuptools
  Successfully installed setuptools-80.9.0 wheel-0.45.1
  Installing build dependencies ... done
  Running command Getting requirements to build wheel
  /tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
  !!

          ********************************************************************************
          Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

          By 2026-Feb-18, you need to update your project and remove deprecated calls
          or your builds will no longer be supported.

          See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
          ********************************************************************************

  !!
    corresp(dist, value, root_dir)
  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'
  Getting requirements to build wheel ... done
  Running command Preparing metadata (pyproject.toml)
  /tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
  !!

          ********************************************************************************
          Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

          By 2026-Feb-18, you need to update your project and remove deprecated calls
          or your builds will no longer be supported.

          See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
          ********************************************************************************

  !!
    corresp(dist, value, root_dir)
  running dist_info
  creating /tmp/pip-modern-metadata-uk_xpu6h/pyg_lib.egg-info
  writing /tmp/pip-modern-metadata-uk_xpu6h/pyg_lib.egg-info/PKG-INFO
  writing dependency_links to /tmp/pip-modern-metadata-uk_xpu6h/pyg_lib.egg-info/dependency_links.txt
  writing requirements to /tmp/pip-modern-metadata-uk_xpu6h/pyg_lib.egg-info/requires.txt
  writing top-level names to /tmp/pip-modern-metadata-uk_xpu6h/pyg_lib.egg-info/top_level.txt
  writing manifest file '/tmp/pip-modern-metadata-uk_xpu6h/pyg_lib.egg-info/SOURCES.txt'
  reading manifest file '/tmp/pip-modern-metadata-uk_xpu6h/pyg_lib.egg-info/SOURCES.txt'
  adding license file 'LICENSE'
  adding license file 'LICENSE_radix_sort'
  writing manifest file '/tmp/pip-modern-metadata-uk_xpu6h/pyg_lib.egg-info/SOURCES.txt'
  creating '/tmp/pip-modern-metadata-uk_xpu6h/pyg_lib-0.4.0.dist-info'
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: pyg_lib
  Running command Building wheel for pyg_lib (pyproject.toml)
  /tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
  !!

          ********************************************************************************
          Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

          By 2026-Feb-18, you need to update your project and remove deprecated calls
          or your builds will no longer be supported.

          See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
          ********************************************************************************

  !!
    corresp(dist, value, root_dir)
  running bdist_wheel
  running build
  running build_py
  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
  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
  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
  Traceback (most recent call last):
    File "/scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 435, in build_wheel
      return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 423, in _build
      return self._build_with_temp_dir(
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 404, in _build_with_temp_dir
      self.run_setup()
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 317, in run_setup
      exec(code, locals())
    File "<string>", line 132, in <module>
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 115, in setup
      return distutils.core.setup(**attrs)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 186, in setup
      return run_commands(dist)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
      dist.run_commands()
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
      self.run_command(cmd)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1102, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/command/bdist_wheel.py", line 370, in run
      self.run_command("build")
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1102, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1102, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 96, in run
      _build_ext.run(self)
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 368, in run
      self.build_extensions()
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions
      self._build_extensions_serial()
    File "/tmp/pip-build-env-yr1fyzul/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial
      self.build_extension(ext)
    File "<string>", line 42, in build_extension
  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.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /scratch/r902a02/.conda/envs/PyG_scratch1/bin/python /scratch/r902a02/.conda/envs/PyG_scratch1/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmps0evk4cl
  cwd: /tmp/pip-req-build-yaxg38hm
  Building wheel for pyg_lib (pyproject.toml) ... error
  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

[akihironitta]

@songsong0425 Replied in pyg-team/pyg-lib#492 (reply in thread).

[fplandes]

I ran into a similar problem and found a surprising solution, after a large amount of time spent on this.

I was trying to install pgy_lib , torch_sparse and torch_scatter into a cluster environement, for which GLIBC version is 2.17 (when some recent builds need 2.27).
Using pip, I was always running into this GLIBC problem.

Using conda, I initially had this problem:

Pins seem to be involved in the conflict. Currently pinned specs:

• python=3.13

downgrading with:
conda install -c conda-forge python=3.12.9
was only postponing the problem, to issue more incompatiblity issues (more details below).

The solution for me was to use an older version of the (mini)conda installer: switching from
wget https://repo.anaconda.com/miniconda/Miniconda3-py312_24.9.2-0-Linux-x86_64.sh
to
wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.10.0-1-Linux-x86_64.sh
all my problems were solved: no pinning and no dependcies issues.

In practice, the older installer uses an older python version, but probably also uses wheels that were compiled using an older (good for my system) version of GLIBC.

Details:
Using the newer miniconda installer and downgrading python (given the first error that says "Currently pinned specs: - python=3.13 ") to python=3.12.9, I then got:

(..)
LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides __glibc >=2.28,<3.0.a0 needed by cudnn-9.8.0.87-h81d5506_0

Could not solve for environment specs
The following packages are incompatible
├─ pin on python 3.12.* =* * is installable and it requires
│ └─ python =3.12 , which can be installed;
├─ pyg-lib = * is not installable because there are no viable options
(..many many lines..)
Pins seem to be involved in the conflict. Currently pinned specs:

• python=3.12

Note that the error messages are not helping much, at least the last one does not.

This solution allows to avoid having to build from source.
It seems that what is missing is wheels that were built using an older GLIBC version.

[akihironitta]

FYI, we don't maintain any conda channels anymore, so you need to install from our index. See https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html.