Mixing package sources caues segfaults when running cli tools with python's subprocess.run

[Enteee]

Describe the bug

When mixing package sources (devenv pkgs and nixpkgs-stable) the following test fails:

To reproduce

For the configuration below, run devenv test.

devenv.nix:

{ pkgs, lib, config, inputs, ... }:

let
  pkgs-stable = import inputs.nixpkgs-stable {
    system = pkgs.stdenv.system;
    config = pkgs.config;
  };
in
{

  # does segfault
  packages = [ pkgs-stable.coreutils ];

  # does not segfault:
  # packages = [ pkgs.coreutils ];

  languages.python.enable = true;

  enterTest = ''
    echo "Running tests"
    python -c 'from subprocess import run; run("uname", check=True)'
  '';
}

devenv.yml

# yaml-language-server: $schema=https://devenv.sh/devenv.schema.json
inputs:
  nixpkgs:
    url: github:cachix/devenv-nixpkgs/rolling
  nixpkgs-stable:
    url: github:NixOS/nixpkgs/nixos-24.05

devenv.lock

{
  "nodes": {
    "devenv": {
      "locked": {
        "dir": "src/modules",
        "lastModified": 1727183374,
        "owner": "cachix",
        "repo": "devenv",
        "rev": "e3f0b77d6c40b28f1bb3411387e314934092ec8e",
        "type": "github"
      },
      "original": {
        "dir": "src/modules",
        "owner": "cachix",
        "repo": "devenv",
        "type": "github"
      }
    },
    "flake-compat": {
      "flake": false,
      "locked": {
        "lastModified": 1696426674,
        "owner": "edolstra",
        "repo": "flake-compat",
        "rev": "0f9255e01c2351cc7d116c072cb317785dd33b33",
        "type": "github"
      },
      "original": {
        "owner": "edolstra",
        "repo": "flake-compat",
        "type": "github"
      }
    },
    "gitignore": {
      "inputs": {
        "nixpkgs": [
          "pre-commit-hooks",
          "nixpkgs"
        ]
      },
      "locked": {
        "lastModified": 1709087332,
        "owner": "hercules-ci",
        "repo": "gitignore.nix",
        "rev": "637db329424fd7e46cf4185293b9cc8c88c95394",
        "type": "github"
      },
      "original": {
        "owner": "hercules-ci",
        "repo": "gitignore.nix",
        "type": "github"
      }
    },
    "nixpkgs": {
      "locked": {
        "lastModified": 1716977621,
        "owner": "cachix",
        "repo": "devenv-nixpkgs",
        "rev": "4267e705586473d3e5c8d50299e71503f16a6fb6",
        "type": "github"
      },
      "original": {
        "owner": "cachix",
        "ref": "rolling",
        "repo": "devenv-nixpkgs",
        "type": "github"
      }
    },
    "nixpkgs-stable": {
      "locked": {
        "lastModified": 1726969270,
        "owner": "NixOS",
        "repo": "nixpkgs",
        "rev": "23cbb250f3bf4f516a2d0bf03c51a30900848075",
        "type": "github"
      },
      "original": {
        "owner": "NixOS",
        "ref": "nixos-24.05",
        "repo": "nixpkgs",
        "type": "github"
      }
    },
    "nixpkgs-stable_2": {
      "locked": {
        "lastModified": 1726969270,
        "owner": "NixOS",
        "repo": "nixpkgs",
        "rev": "23cbb250f3bf4f516a2d0bf03c51a30900848075",
        "type": "github"
      },
      "original": {
        "owner": "NixOS",
        "ref": "nixos-24.05",
        "repo": "nixpkgs",
        "type": "github"
      }
    },
    "pre-commit-hooks": {
      "inputs": {
        "flake-compat": "flake-compat",
        "gitignore": "gitignore",
        "nixpkgs": [
          "nixpkgs"
        ],
        "nixpkgs-stable": "nixpkgs-stable_2"
      },
      "locked": {
        "lastModified": 1726745158,
        "owner": "cachix",
        "repo": "pre-commit-hooks.nix",
        "rev": "4e743a6920eab45e8ba0fbe49dc459f1423a4b74",
        "type": "github"
      },
      "original": {
        "owner": "cachix",
        "repo": "pre-commit-hooks.nix",
        "type": "github"
      }
    },
    "root": {
      "inputs": {
        "devenv": "devenv",
        "nixpkgs": "nixpkgs",
        "nixpkgs-stable": "nixpkgs-stable",
        "pre-commit-hooks": "pre-commit-hooks"
      }
    }
  },
  "root": "root",
  "version": 7
}

Make sure to include full logs and what you expected to happen.

Version

devenv 1.1.0 (x86_64-linux)

[Enteee]

I tried debugging this a bit and seems like the segfault happens in:

Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x0000000000000000 in ?? ()
(gdb) bt
#0  0x0000000000000000 in ?? ()
#1  0x000070154334af69 in gettimeofday () from /nix/store/7v7c61ikm7cbd3kbimk9qr8h7pdmyccn-manylinux2014/lib/libc.so.6
#2  0x0000701543539c34 in _dl_relocate_object () from /nix/store/r8qsxm85rlxzdac7988psm7gimg4dl3q-glibc-2.39-52/lib/ld-linux-x86-64.so.2
#3  0x0000701543549d69 in dl_main () from /nix/store/r8qsxm85rlxzdac7988psm7gimg4dl3q-glibc-2.39-52/lib/ld-linux-x86-64.so.2
#4  0x00007015435465f3 in _dl_sysdep_start () from /nix/store/r8qsxm85rlxzdac7988psm7gimg4dl3q-glibc-2.39-52/lib/ld-linux-x86-64.so.2
#5  0x0000701543547d8e in _dl_start () from /nix/store/r8qsxm85rlxzdac7988psm7gimg4dl3q-glibc-2.39-52/lib/ld-linux-x86-64.so.2
#6  0x0000701543546bd8 in _start () from /nix/store/r8qsxm85rlxzdac7988psm7gimg4dl3q-glibc-2.39-52/lib/ld-linux-x86-64.so.2
#7  0x0000000000000002 in ?? ()
#8  0x00007ffc3bfdf46f in ?? ()
#9  0x00007ffc3bfdf475 in ?? ()
#10 0x0000000000000000 in ?? ()

[Enteee]

If i add pkgs-stable.coreutils to the packages = [ .. ] array poetry install starts failing with segfaults in uname :)

[domenkozar]

languages.python.manylinux.enable = false;

[Enteee]

Thank you @domenkozar.

Yes, this solves it. But I don't really understand why...
How does disabling a layer that should improve compatibility actually makes my python env more compatible with different versions of packages?

[Enteee]

Thank you @domenkozar.

Yes, this solves it. But I don't really understand why... How does disabling a layer that should improve compatibility actually makes my python env more compatible with different versions of packages?

mhmm.. actually no. Looks like i am still seeing this issue when I am trying to run a cli in a test with pytest. Let my try to derive a new minimal failing example.

[Enteee]

ok.. i was struggling quite a bit trying to reproduce this in a minimal example. But I could easily reproduce this issue in my project. I tried copying over all lock files and making my minimal example very similar to my project.

Turns out after I rm -rf .venv in my project - I can no longer reproduce this in my project either..