2 minute read


AlphaFold 2 has brought unprecented opportunities to the field of (structural) biology. But how to run it with the all imaginable handicaps at once? After some days of debugging, I managed to run AlphaFold2 (and any other GPGPU program** on my EXWM-NixOS using an nvidia-eGPU while having my X-Server still running on my intel GPU. Let’s get started.

Required steps

eGPU authorization

As explained here, you need to authorize the eGPU such that it is allowed to access you PCIe-bus. This can also be done using the program bolt, or in more user-friendly environments like GNOME, a dialog will nicely ask you to authorize after plugging in the eGPU.

echo 1 > /sys/bus/thunderbolt/devices/0-0/0-1/authorized

NixOS workarounds

As discussed in this GitHub issue, there are several Nix-configurations to make.

Load Nvidia libraries

Intel does not load the required nvidia libraries, so they have to be added manually

{ config, ... }:
  nvidia_x11 = config.boot.kernelPackages.nvidia_x11;
  nvidia_gl = nvidia_x11.out;
  nvidia_gl_32 = nvidia_x11.lib32;
  boot.extraModulePackages = [ nvidia_x11 ];
  environment.systemPackages = [ nvidia_x11 ];

  hardware.opengl = {
    enable = true;
    driSupport = true;
    driSupport32Bit = true;
    extraPackages = [ nvidia_gl ];
    extraPackages32 = [ nvidia_gl_32 ];

Fix libnvidia-container not finding nvidia-smi and other nvidia binaries.

When running your X-server on intel (internal GPU), nvidia binaries are not propagated in /run/nvida-docker/bin (note: when X-server runs on nvidia, they are linked to /run/nvida-docker/bin from the nix-store (see code)). nvidia-docker looks for the binaries in that folder though.

This PR works around this issue, by linking the binaries into docker not via the /run/nvidia-docker path, but via the nix-store directly.


The relevant line is the following, patching the lbinvdia-container source code:

sed -i "s#/run/nvidia-docker/bin:/run/nvidia-docker/extras/bin#${linuxPackages.nvidia_x11.bin}/origBin#" src/nvc_info.c

Use the fixed version in my NixOS configuration

While this patch is not merged, the following overlay can pull the modified libnvidia-container code into your configuration:

    mkNvidiaContainerPkg = { name, containerRuntimePath, configTemplate, additionalPaths ? [] }:
        nvidia-container-runtime = pkgs.callPackage "${inputs.nixpkgs}/pkgs/applications/virtualization/nvidia-container-runtime" {
          inherit containerRuntimePath configTemplate;
      in pkgs.symlinkJoin {
        inherit name;
        paths = [
          # (callPackage ../applications/virtualization/libnvidia-container { })
          (pkgs.callPackage "${inputs.nixpkgs-local}/pkgs/applications/virtualization/libnvidia-container" { })  # this is the patched version
          (pkgs.callPackage "${inputs.nixpkgs}/pkgs/applications/virtualization/nvidia-container-toolkit" {
            inherit nvidia-container-runtime;
        ] ++ additionalPaths;

Configure your X Server to run on intel GPU and to load install nvidia drivers

  system.nixos.tags = [ "with-nvidia-egpu" ];

  services.hardware.bolt.enable = true;
  services.xserver.videoDrivers = [ "intel" ];
  boot.extraModulePackages = [ pkgs.linuxPackages.nvidia_x11 ];
  environment.systemPackages = [ pkgs.linuxPackages.nvidia_x11 ];
  boot.blacklistedKernelModules = [ "nouveau" "nvidia_drm" "nvidia_modeset" "nvidia" ];
  # This has been mentioned before in the blog post
  hardware.opengl = {
    enable = true;
    driSupport = true;
    extraPackages = with pkgs; [
      pkgs.linuxPackages.nvidia_x11.out  # required for nvidia-docker
    extraPackages32 = [ pkgs.linuxPackages.nvidia_x11.lib32 ];
  # not sure if these are useful/required
  boot.extraModprobeConfig = "options nvidia \"NVreg_DynamicPowerManagement=0x02\"\n";
  services.udev.extraRules = ''
    # Remove NVIDIA USB xHCI Host Controller devices, if present
    ACTION=="add", SUBSYSTEM=="pci", ATTR{vendor}=="0x10de", ATTR{class}=="0x0c0330", ATTR{remove}="1"

    # Remove NVIDIA USB Type-C UCSI devices, if present
    ACTION=="add", SUBSYSTEM=="pci", ATTR{vendor}=="0x10de", ATTR{class}=="0x0c8000", ATTR{remove}="1"

    # Remove NVIDIA Audio devices, if present
    ACTION=="add", SUBSYSTEM=="pci", ATTR{vendor}=="0x10de", ATTR{class}=="0x040300", ATTR{remove}="1"

    # Enable runtime PM for NVIDIA VGA/3D controller devices on driver bind
    ACTION=="bind", SUBSYSTEM=="pci", ATTR{vendor}=="0x10de", ATTR{class}=="0x030000", TEST=="power/control", ATTR{power/control}="auto"
    ACTION=="bind", SUBSYSTEM=="pci", ATTR{vendor}=="0x10de", ATTR{class}=="0x030200", TEST=="power/control", ATTR{power/control}="auto"

    # Disable runtime PM for NVIDIA VGA/3D controller devices on driver unbind
    ACTION=="unbind", SUBSYSTEM=="pci", ATTR{vendor}=="0x10de", ATTR{class}=="0x030000", TEST=="power/control", ATTR{power/control}="on"
    ACTION=="unbind", SUBSYSTEM=="pci", ATTR{vendor}=="0x10de", ATTR{class}=="0x030200", TEST=="power/control", ATTR{power/control}="on"

Good luck