CPU installation

[wangjiawen2013]

Hi,
I tried Protenix server and it worked very well.

We are using bytedance's volcano cloud for about two years ! We also has a local centos server.

I installed protenix in our local server sucessfully but failed to run because the GPU driver in our server is outdated. Then I tried python3 setup.py develop --cpu, however the following error occurred:

!!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  easy_install.initialize_options(self)
/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:79: SetuptoolsDeprecationWarning: setup.py install is deprecated.

and this error:

detected new path './py_cpuinfo-9.0.0-py3.11.egg'
Traceback (most recent call last):
  File "/home/wangjw/data/work/Protenix/setup.py", line 35, in <module>
    setup(
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/__init__.py", line 117, in setup
    return distutils.core.setup(**attrs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 186, in setup
    return run_commands(dist)
           ^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
    dist.run_commands()
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 983, in run_commands
    self.run_command(cmd)
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/dist.py", line 999, in run_command
    super().run_command(command)
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
    cmd_obj.run()
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/command/develop.py", line 35, in run
    self.install_for_development()
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/command/develop.py", line 127, in install_for_development
    self.process_distribution(None, self.dist, not self.no_deps)
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/command/easy_install.py", line 787, in process_distribution
    distros = WorkingSet([]).resolve(
              ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/pkg_resources/__init__.py", line 888, in resolve
    dist = self._resolve_dist(
           ^^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/pkg_resources/__init__.py", line 924, in _resolve_dist
    dist = best[req.key] = env.best_match(
                           ^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1262, in best_match
    return self.obtain(req, installer)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1298, in obtain
    return installer(requirement) if installer else None
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/command/easy_install.py", line 709, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/command/easy_install.py", line 738, in install_item
    self.process_distribution(spec, dist, deps)
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/command/easy_install.py", line 769, in process_distribution
    self.install_egg_scripts(dist)
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/command/develop.py", line 152, in install_egg_scripts
    return easy_install.install_egg_scripts(self, dist)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/setuptools/command/easy_install.py", line 637, in install_egg_scripts
    dist, script_name, dist.get_metadata('scripts/' + script_name)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1694, in get_metadata
    return value.decode('utf-8')
           ^^^^^^^^^^^^^^^^^^^^^
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xac in position 25: invalid start byte in scripts/ninja file at path: /home/wangjw/programs/miniconda3/envs/af3/lib/python3.11/site-packages/ninja-1.11.1.3-py3.11-linux-x86_64.egg/EGG-INFO/scripts/ninja

[wangjiawen2013]

Could you point out what's wrong with the CPU installation ? I know maybe we cannot run protenix smoothly on our local server because the computation speed limitation, but I want to try. We have no GPU avaible now, perhaps we can train our small decoy dataset using protenix with CPU.

[zhangyuxuann]

@wangjiawen2013 can you try

pip uninstall ninja
pip install ninja

[wangjiawen2013]

@zhangyuxuann
I installed protenix successfully finally by the following steps:

pip install ninja
conda install conda-forge::cudatoolkit
python3 setup.py develop --cpu

Then test the installation with protenix predict --help. It will report that some library files cannot be find. Then copy the missing library files to the libary path that we use.

But I still cannot run protenix on cpu, here is the error:

RuntimeError: The NVIDIA driver on your system is too old (found version 11070). Please update your GPU driver by downloading and installing a new version from the URL: http://www.nvidia.com/Download/index.aspx Alternatively, go to: https://pytorch.org to install a PyTorch version that has been compiled with your version of the CUDA driver.

Maybe 'cpu only' means that there are no GPU on our server. If we want to use the cpu only local installation, we must make sure that there are on GPU on the server (we have an nvidia 3070Ti GPU on our server), otherwise protenix will detect and use the GPU automatically.