Hi Matthew,
That error means, as you correctly noted, spheres have entered invalid subdomains (the simulation world is divided into subdomains for contact detection purposes), most likely out of bounds. This error admittedly did not specify the cause for that, but since it happens at the start, it is usually either because of the particles being initialized out-of-bound, or some simulation settings that will immediately disrupt the simulation (such as large initial particle penetration, initial particle--boundary overlap...), causing the particles to move at extreme velocities and go out-of-bound.
I did not run your script, but I can see a few leads following what I said. For example, a plane is created at y=480 but faces positive y. In that case, all particles that have y coordinates lower than 480 will have contacts with this plane, and likely very large initial penetrations (for example 280, for a particle setting at y=200). This should kill the simulation. There could be other problems. You can debug based on the rendering of the initial frame. You can also start from a minimal working script, then gradually add the suspicious settings to discover which is creating problems.
By the way, it looks like you are running DEM simulations involving a few prescribed meshes.
Chrono DEM-Engine can handle this better, giving you clearer error information, more complete mesh motion controls and of course, support for complex particles.
Thank you,
Ruochun