Using custom Python from nixpkgs-python results in an interpreter unable to find glibc (I think)

[mcdonc]

  languages.python = {
    enable = true;
    version = "3.11.6";
    venv = {
      enable = true;
    };
  };

inputs:
  nixpkgs:
    url: github:NixOS/nixpkgs/nixos-23.11
  nixpkgs-python:
    url: github:cachix/nixpkgs-python
  devenv:
    url: github:mcdonc/devenv/python-rewrite

allowUnfree: true

(this only works if you use the nixpkgs-python cachix cache or turn off sandboxing, see #901)

devenv shell
Building shell ...
trace: warning: For cachix.push and cachix.pull attributes to have an effect,
upgrade to devenv 1.0 or later.

Entering shell ...

Python interpreter changed, rebuilding Python venv...
/nix/store/m29jrr9cy9wg9kgy7k1dyr0gc44a5r43-python3-3.11.6-env/bin/python3.11 -m venv --upgrade-deps /home/chrism/projects/apex/eao_dash/.devenv/state/venv
/nix/store/3w7xj32jhxqhkvn66x67vql9lzmbffyw-python3-3.11.6/bin/python3.11: error while loading shared libraries: __vdso_gettimeofday: invalid mode for dlopen(): Invalid argument
bash: /home/chrism/projects/apex/eao_dash/.devenv/state/venv/.devenv_interpreter: No such file or directory
bash: /home/chrism/projects/apex/eao_dash/.devenv/state/venv/bin/activate: No such file or directory
bash: /home/chrism/projects/apex/eao_dash/.devenv/state/venv/bin/pip: No such file or directory
✨ devenv 0.6.3 is out of date. Please update to 1.0: https://devenv.sh/getting-started/#installation
(devenv) 
[chrism@thinknix512:~/projects/apex/eao_dash]$ /nix/store/m29jrr9cy9wg9kgy7k1dyr0gc44a5r43-python3-3.11.6-env/bin/python3.11
/nix/store/3w7xj32jhxqhkvn66x67vql9lzmbffyw-python3-3.11.6/bin/python3.11: error while loading shared libraries: __vdso_gettimeofday: invalid mode for dlopen(): Invalid argument
(devenv) 

[mcdonc]

Note that working with nixpkgs-python directly works fine:

❯ nix build '.#"3.11.6"'
❯ ./result/bin/python -c "pass"

So it likely has something to do with LD_LIBRARY_PATH or possibly the Python binary wrappers.

[mcdonc]

It's the Python binary wrappers:

❯ devenv shell
Building shell ...
trace: warning: For cachix.push and cachix.pull attributes to have an effect,
upgrade to devenv 1.0 or later.

Entering shell ...

Python interpreter changed, rebuilding Python venv...
/nix/store/m29jrr9cy9wg9kgy7k1dyr0gc44a5r43-python3-3.11.6-env/bin/python3.11 -m venv --upgrade-deps /home/chrism/projects/apex/eao_dash/.devenv/state/venv
/nix/store/3w7xj32jhxqhkvn66x67vql9lzmbffyw-python3-3.11.6/bin/python3.11: error while loading shared libraries: __vdso_gettimeofday: invalid mode for dlopen(): Invalid argument
bash: /home/chrism/projects/apex/eao_dash/.devenv/state/venv/.devenv_interpreter: No such file or directory
bash: /home/chrism/projects/apex/eao_dash/.devenv/state/venv/bin/activate: No such file or directory
bash: /home/chrism/projects/apex/eao_dash/.devenv/state/venv/.devenv_requirements: No such file or directory
Requirements changed, running pip install -r /nix/store/2cjacq6j9ms8f588fy4395h3d246gadk-requirements.txt...
bash: /home/chrism/projects/apex/eao_dash/.devenv/state/venv/bin/pip: No such file or directory
✨ devenv 0.6.3 is out of date. Please update to 1.0: https://devenv.sh/getting-started/#installation
(devenv) 
[chrism@thinknix512:~/projects/apex/eao_dash]$ /nix/store/m29jrr9cy9wg9kgy7k1dyr0gc44a5r43-python3-3.11.6-env/bin/python3.11
/nix/store/3w7xj32jhxqhkvn66x67vql9lzmbffyw-python3-3.11.6/bin/python3.11: error while loading shared libraries: __vdso_gettimeofday: invalid mode for dlopen(): Invalid argument
(devenv) 
[chrism@thinknix512:~/projects/apex/eao_dash]$ 
(devenv) 
[chrism@thinknix512:~/projects/apex/eao_dash]$ /nix/store/3w7xj32jhxqhkvn66x67vql9lzmbffyw-python3-3.11.6/bin/python3.11
Python 3.11.6 (main, Oct  2 2023, 13:45:54) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> 
(devenv) 
[chrism@thinknix512:~/projects/apex/eao_dash]$ 

[mcdonc]

Disabling the inclusion of pkgs.pythonManylinuxPackages.manylinux2014Package in the definition of libraries allows the wrapper to work.

I suspect that putting manylinux on the LD_LIBRARY_PATH is the major rationale for the wrapper because libraries just kinda work anyway, but I'm not sure how it would work? nixpkgs-python is going to produce things that link to some glibc, and the manylinux wrapper is going to put another glibc on the LD_LIBRARY_PATH that will be found first.

I'm going to try to hit up @domenkozar in the devenv element room sometime this week so I can understand how this might be meant to work.

[mcdonc]

Until this is fixed, adding this to your devenv.nix:

languages.python.manylinux.enable = false;

Will work around it.

[mcdonc]

Irritating. Although numpy installs as a "manylinux" wheel, it actually has a dependency on a non-manylinux library (zlib):

[chrism@optinix:~/projects/devenv/tmp/.devenv/state/venv/lib/python3.11/site-packages/numpy]$ find . -name "*.so"|xargs ldd|grep "not found"
	libz.so.1 => not found
	libz.so.1 => not found
	libz.so.1 => not found

[mcdonc]

Note that doing some shenanigans to synchronize nixpkg-python's nixpkgs input to the nixpkgs input produces a working wrapper (it can create the venv):

inputs:
  nixpkgs:
    url: github:NixOS/nixpkgs/nixos-23.11
  nixpkgs-python:
    url: github:cachix/nixpkgs-python
    inputs:
      nixpkgs:
        follows: nixpkgs

However, this causes at least one bizarre behavior when trying to use various Python 3.11 packages. In one case, trying to use the nixpkgs version of concurrent.futures tells me I have a Python compiled without semaphore support when I try to use version: 3.11.6 in the devenv config.

[mcdonc]

#920 will fix this issue.

[domenkozar]

#920 is merged!