opencv4 and scipy cause glibc version conflicts with cudaSupport

[RuRo]

Describe the bug

Trying to import opencv4 and scipy with cuda can cause glibc version conflicts.

Steps To Reproduce

{
  inputs.nixpkgs.url = "github:nixos/nixpkgs/0396d3b0fb7f62ddc79a506ad3e6124f01d2ed0a";

  outputs = { nixpkgs, ... }: let
    reproduction = { pkgs, ... }: {
      nixpkgs.config = {
        allowUnfree = true;
        cudaSupport = true;

        # the cudaCapabilities line is probably not required for reproduction,
        # but I specify just a single capability version to reduce build time
        cudaCapabilities = [ "8.6" ];
      };

      environment.systemPackages = [(pkgs.python3.withPackages (ps: [
        ps.opencv4
        ps.scipy
      ]))];
    };
  in
  {
    nixosConfigurations.testing = nixpkgs.lib.nixosSystem {
      system = "x86_64-linux";
      modules = [
        { users.users.root.password = ""; }
        reproduction
      ];
    };
  };
}

nix build .#nixosConfigurations.testing.config.system.build.vm
result/bin/run-nixos-vm -nographic

Login as root (the password is empty) and then run

python -c "import cv2" # this is OK
python -c "import scipy.fft" # this is OK
python -c "import scipy.fft; import cv2" # this is also OK

python -c "import cv2; import scipy.fft" # Boom!

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/nix/store/5phig9ydshwkaka96xn6llxpfcsjyzrl-python3-3.10.12-env/lib/python3.10/site-packages/scipy/fft/__init__.py", line 92, in <module>
    from ._helper import next_fast_len
  File "/nix/store/5phig9ydshwkaka96xn6llxpfcsjyzrl-python3-3.10.12-env/lib/python3.10/site-packages/scipy/fft/_helper.py", line 3, in <module>
    from ._pocketfft import helper as _helper
  File "/nix/store/5phig9ydshwkaka96xn6llxpfcsjyzrl-python3-3.10.12-env/lib/python3.10/site-packages/scipy/fft/_pocketfft/__init__.py", line 3, in <module>
    from .basic import *
  File "/nix/store/5phig9ydshwkaka96xn6llxpfcsjyzrl-python3-3.10.12-env/lib/python3.10/site-packages/scipy/fft/_pocketfft/basic.py", line 6, in <module>
    from . import pypocketfft as pfft
ImportError: /nix/store/pfx4gg15nllsa6cwfhjnink1jr35dpfq-gcc-11.3.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /nix/store/5phig9ydshwkaka96xn6llxpfcsjyzrl-python3-3.10.12-env/lib/python3.10/site-package)

Expected behavior

No crashes

Notify maintainers

I am not really sure, which of the 3 components in the reproduction is actually responsible (if any), so I am pinging the maintainers of all three.

cuda: @ConnorBaker @samuela @SomeoneSerge @NixOS/cuda-maintainers
opencv4: @basvandijk
scipy: @FRidh @doronbehar

Also, this might be related to #220341 #226165

[ConnorBaker]

Yes, that looks to be another need for #226165 :(

Tangentially related — does GPU pass through work with NixOS VMs?

[RuRo]

Tangentially related — does GPU pass through work with NixOS VMs?

I have no idea, sorry. I am using the VMs purely for creating minimal reproducible examples, not actually running stuff on them.

[SomeoneSerge]

As per #226165 (comment), maybe you start seeing if it might suffice to use cudaPackages.stdenv instead of

nixpkgs/pkgs/development/libraries/opencv/4.x.nix

Line 263 in f8387ff

stdenv.mkDerivation {

python -c "import cv2; import scipy.fft" # Boom!

...awesome, I think we should add this to passthru.tests (note this doesn't require gpu access)