Problems with the installation of pyg-lib

[SulafahKhaled]

Hello guys,
I hope you are doing great.
I am facing an issue with installing pyg-lib, I am trying to run a code from another github. However, it is asking for neighbor sampler. When trying to install it it asks for pyg-lib.
I used the following link to install it :
!pip install git+https://github.com/pyg-team/pyg-lib.git

and it generated an error saying:

Collecting git+https://github.com/pyg-team/pyg-lib.git
  Cloning https://github.com/pyg-team/pyg-lib.git to /tmp/pip-req-build-53kmyika
  Running command git clone --filter=blob:none --quiet https://github.com/pyg-team/pyg-lib.git /tmp/pip-req-build-53kmyika
  Resolved https://github.com/pyg-team/pyg-lib.git to commit 6dc038578c6a9942b26c98a489c02a2ef16330e9
  Running command git submodule update --init --recursive -q
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: pyg-lib
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel 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.
  Building wheel for pyg-lib (setup.py) ... error
  ERROR: Failed building wheel for pyg-lib
  Running setup.py clean for pyg-lib
Failed to build pyg-lib
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (pyg-lib)

Trying to solve this problem, I searched online and someone suggested installing torch-scatter and other libraries which I tried using :

!pip install torch torchvision torchaudio torch-geometric torch-scatter torch-sparse torch-cluster --extra-index-url https://data.pyg.org/whl/
!pip install scikit-learn pandas tqdm

and it generated the following error :

Looking in indexes: https://pypi.org/simple, https://data.pyg.org/whl/
Collecting torch
  Using cached torch-2.5.1-cp311-cp311-manylinux1_x86_64.whl.metadata (28 kB)
Collecting torchvision
  Using cached torchvision-0.20.1-cp311-cp311-manylinux1_x86_64.whl.metadata (6.1 kB)
Collecting torchaudio
  Using cached torchaudio-2.5.1-cp311-cp311-manylinux1_x86_64.whl.metadata (6.4 kB)
Requirement already satisfied: torch-geometric in /usr/local/lib/python3.11/site-packages (2.6.1)
Collecting torch-scatter
  Using cached torch_scatter-2.1.2.tar.gz (108 kB)
  error: subprocess-exited-with-error
  
  × python setup.py egg_info 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.
  Preparing metadata (setup.py) ... error
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Requirement already satisfied: scikit-learn in /usr/local/lib/python3.11/site-packages (1.6.1)
Requirement already satisfied: pandas in /usr/local/lib/python3.11/site-packages (2.2.3)
Requirement already satisfied: tqdm in /usr/local/lib/python3.11/site-packages (4.67.1)
Requirement already satisfied: numpy>=1.19.5 in /usr/local/lib/python3.11/site-packages (from scikit-learn) (2.2.2)
Requirement already satisfied: scipy>=1.6.0 in /usr/local/lib/python3.11/site-packages (from scikit-learn) (1.15.1)
Requirement already satisfied: joblib>=1.2.0 in /usr/local/lib/python3.11/site-packages (from scikit-learn) (1.4.2)
Requirement already satisfied: threadpoolctl>=3.1.0 in /usr/local/lib/python3.11/site-packages (from scikit-learn) (3.5.0)
Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.11/site-packages (from pandas) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.11/site-packages (from pandas) (2024.2)
Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.11/site-packages (from pandas) (2025.1)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas) (1.17.0)

I am not sure what to do, please help. By the way, I used this same method a month ago and it worked(:

[akihironitta]

Is this all the output from the command you ran? The logs should have more info.

Would you mind running this and providing the full error message?

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

[SulafahKhaled]

this was all of it.
Sure, Also it might be worth mentioning that I am running a conda env recommended by the paper I am using their github.
this is the code they have recommended :

`!pip install -q condacolab
import condacolab
condacolab.install()
!conda --version

!conda create -n cgmega python=3.8.12 -y

#Activate the environment and install the required packages
# You must use `source` to activate the environment for shell commands in Colab
!source activate cgmega && conda install pytorch==1.9.1 -c pytorch -y

# Install the required Python packages using pip
!source activate cgmega && pip install torch_geometric==2.0.3 transformers wandb jupyter

# Install PyG-specific packages for PyTorch 1.9.1 with CUDA 11.3
!source activate cgmega && pip install torch_scatter -f https://data.pyg.org/whl/torch-1.9.1+cu113.html
!source activate cgmega && pip install torch_sparse==0.6.12 -f https://data.pyg.org/whl/torch-1.9.1+cu113.html
!source activate cgmega && pip install git+https://github.com/pyg-team/pyg-lib.git
# Verify the environment
!source activate cgmega && python -c "import torch; print(torch.__version__)"
!source activate cgmega && python -c "import torch_geometric; print(torch_geometric.__version__)"`

after running the command you suggested this is the output :

Collecting ninja
  Downloading ninja-1.11.1.3-py3-none-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (5.3 kB)
Requirement already satisfied: wheel in /usr/local/lib/python3.11/site-packages (0.45.1)
Downloading ninja-1.11.1.3-py3-none-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (422 kB)
Installing collected packages: ninja
Successfully installed ninja-1.11.1.3
Using pip 24.3.1 from /usr/local/lib/python3.11/site-packages/pip (python 3.11)
Collecting git+https://github.com/pyg-team/pyg-lib.git
  Cloning https://github.com/pyg-team/pyg-lib.git to /tmp/pip-req-build-58s85yac
  Running command git version
  git version 2.34.1
  Running command git clone --filter=blob:none https://github.com/pyg-team/pyg-lib.git /tmp/pip-req-build-58s85yac
  Cloning into '/tmp/pip-req-build-58s85yac'...
  Running command git rev-parse HEAD
  6dc038578c6a9942b26c98a489c02a2ef16330e9
  Resolved https://github.com/pyg-team/pyg-lib.git to commit 6dc038578c6a9942b26c98a489c02a2ef16330e9
  Running command git submodule update --init --recursive -q
  Running command git rev-parse HEAD
  6dc038578c6a9942b26c98a489c02a2ef16330e9
  Running command python setup.py egg_info
  running egg_info
  creating /tmp/pip-pip-egg-info-y44baa9k/pyg_lib.egg-info
  writing /tmp/pip-pip-egg-info-y44baa9k/pyg_lib.egg-info/PKG-INFO
  writing dependency_links to /tmp/pip-pip-egg-info-y44baa9k/pyg_lib.egg-info/dependency_links.txt
  writing requirements to /tmp/pip-pip-egg-info-y44baa9k/pyg_lib.egg-info/requires.txt
  writing top-level names to /tmp/pip-pip-egg-info-y44baa9k/pyg_lib.egg-info/top_level.txt
  writing manifest file '/tmp/pip-pip-egg-info-y44baa9k/pyg_lib.egg-info/SOURCES.txt'
  reading manifest file '/tmp/pip-pip-egg-info-y44baa9k/pyg_lib.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no previously-included files matching '*' found under directory 'docs'
  warning: no previously-included files matching '*' found under directory 'benchmark'
  adding license file 'LICENSE'
  adding license file 'LICENSE_radix_sort'
  writing manifest file '/tmp/pip-pip-egg-info-y44baa9k/pyg_lib.egg-info/SOURCES.txt'
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: pyg_lib
  Running command python setup.py bdist_wheel
  running bdist_wheel
  running build
  running build_py
  creating build/lib.linux-x86_64-cpython-311/pyg_lib
  copying pyg_lib/home.py -> build/lib.linux-x86_64-cpython-311/pyg_lib
  copying pyg_lib/testing.py -> build/lib.linux-x86_64-cpython-311/pyg_lib
  copying pyg_lib/_triton.py -> build/lib.linux-x86_64-cpython-311/pyg_lib
  copying pyg_lib/__init__.py -> build/lib.linux-x86_64-cpython-311/pyg_lib
  creating build/lib.linux-x86_64-cpython-311/pyg_lib/ops
  copying pyg_lib/ops/scatter_reduce.py -> build/lib.linux-x86_64-cpython-311/pyg_lib/ops
  copying pyg_lib/ops/__init__.py -> build/lib.linux-x86_64-cpython-311/pyg_lib/ops
  creating build/lib.linux-x86_64-cpython-311/pyg_lib/sampler
  copying pyg_lib/sampler/__init__.py -> build/lib.linux-x86_64-cpython-311/pyg_lib/sampler
  creating build/lib.linux-x86_64-cpython-311/pyg_lib/classes
  copying pyg_lib/classes/__init__.py -> build/lib.linux-x86_64-cpython-311/pyg_lib/classes
  creating build/lib.linux-x86_64-cpython-311/pyg_lib/partition
  copying pyg_lib/partition/__init__.py -> build/lib.linux-x86_64-cpython-311/pyg_lib/partition
  running build_ext
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/tmp/pip-req-build-58s85yac/setup.py", line 133, in <module>
      setup(
    File "/usr/local/lib/python3.11/site-packages/setuptools/__init__.py", line 117, in setup
      return distutils.core.setup(**attrs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 186, in setup
      return run_commands(dist)
             ^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
      dist.run_commands()
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 983, in run_commands
      self.run_command(cmd)
    File "/usr/local/lib/python3.11/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
      cmd_obj.run()
    File "/usr/local/lib/python3.11/site-packages/setuptools/command/bdist_wheel.py", line 379, in run
      self.run_command("build")
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
      self.distribution.run_command(command)
    File "/usr/local/lib/python3.11/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
      cmd_obj.run()
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 136, in run
      self.run_command(cmd_name)
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
      self.distribution.run_command(command)
    File "/usr/local/lib/python3.11/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
      cmd_obj.run()
    File "/usr/local/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 99, in run
      _build_ext.run(self)
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 365, in run
      self.build_extensions()
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 481, in build_extensions
      self._build_extensions_serial()
    File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 507, in _build_extensions_serial
      self.build_extension(ext)
    File "/tmp/pip-req-build-58s85yac/setup.py", line 42, in build_extension
      import torch
  ModuleNotFoundError: No module named 'torch'
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel 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: /usr/local/bin/python3.11 -u -c '
  exec(compile('"'"''"'"''"'"'
  # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
  #
  # - It imports setuptools before invoking setup.py, to enable projects that directly
  #   import from `distutils.core` to work with newer packaging standards.
  # - It provides a clear error message when setuptools is not installed.
  # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
  #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
  #     manifest_maker: standard file '"'"'-c'"'"' not found".
  # - It generates a shim setup.py, for handling setup.cfg-only projects.
  import os, sys, tokenize
  
  try:
      import setuptools
  except ImportError as error:
      print(
          "ERROR: Can not execute `setup.py` since setuptools is not available in "
          "the build environment.",
          file=sys.stderr,
      )
      sys.exit(1)
  
  __file__ = %r
  sys.argv[0] = __file__
  
  if os.path.exists(__file__):
      filename = __file__
      with tokenize.open(__file__) as f:
          setup_py_code = f.read()
  else:
      filename = "<auto-generated setuptools caller>"
      setup_py_code = "from setuptools import setup; setup()"
  
  exec(compile(setup_py_code, filename, "exec"))
  '"'"''"'"''"'"' % ('"'"'/tmp/pip-req-build-58s85yac/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-mlz203em
  cwd: /tmp/pip-req-build-58s85yac/
  Building wheel for pyg_lib (setup.py) ... error
  ERROR: Failed building wheel for pyg_lib
  Running setup.py clean for pyg_lib
  Running command python setup.py clean
  running clean
  removing 'build/lib.linux-x86_64-cpython-311' (and everything under it)
  'build/bdist.linux-x86_64' does not exist -- can't clean it
  'build/scripts-3.11' does not exist -- can't clean it
  removing 'build'
Failed to build pyg_lib
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (pyg_lib)

Thank you

[akihironitta]

The PyTorch version is too old for us to support. Also, as your error suggests:

  ModuleNotFoundError: No module named 'torch'

you don't have PyTorch installed. You need to make sure you install PyTorch before installing pyg-lib.

[SulafahKhaled]

what version of Pytorch should I install to be compatible with pyg-lib? Also, I installed torch-geometric only, does it need to have torch as well?

`!pip install -q condacolab
import condacolab
condacolab.install()
!conda --version

!conda create -n cgmega python=3.8.12 -y

#Activate the environment and install the required packages
# You must use `source` to activate the environment for shell commands in Colab
!source activate cgmega && conda install pytorch==1.9.1 -c pytorch -y

# Install the required Python packages using pip
!source activate cgmega && pip install torch
!source activate cgmega && pip install torch_geometric==2.0.3 transformers wandb jupyter

# Install PyG-specific packages for PyTorch 1.9.1 with CUDA 11.3
!source activate cgmegapip install torch torchvision torchaudio torch-geometric torch-scatter torch-sparse torch-cluster --extra-index-url https://data.pyg.org/whl/
!source activate cgmegapip install scikit-learn pandas tqdm
#!source activate cgmega && pip install torch_scatter -f https://data.pyg.org/whl/torch-1.9.1+cu113.html
#!source activate cgmega && pip install torch_sparse==0.6.12 -f https://data.pyg.org/whl/torch-1.9.1+cu113.html
!source activate cgmega && pip install ninja wheel
!source activate cgmega && pip install --verbose git+https://github.com/pyg-team/pyg-lib.git

# Verify the environment
!source activate cgmega && python -c "import torch; print(torch.__version__)"
!source activate cgmega && python -c "import torch_geometric; print(torch_geometric.__version__)"`

Do you think this will solve the problem ?

[akihironitta]

what version of Pytorch should I install to be compatible with pyg-lib?

See https://github.com/pyg-team/pyg-lib/#installation

Also, I installed torch-geometric only, does it need to have torch as well?

Yes, pyg-lib requires torch.