After some investigating, I have found that if I log out, switch to TTY then 
run startx, I get the same issue. However I noticed that if I run sudo startx, 
Vulkan works, and it still works after logging out and running startx as a 
normal user, until the computer is rebooted. Then I tried logging in as root 
from GDM and I got the same result.
Something is probably not being initialized properly when logging in as a 
non-root user.
I think the affected package is actually xinit, but I'm not sure.

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https://bugs.launchpad.net/bugs/1769857

Title:
  Vulkan not working if nvidia-drm.modeset=1 is set and gdm3 is used
  (Optimus)

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