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The errors you are seeing are independent of the shading method you are using (they will appear for both PixelCounting and PolygonClipping. These errors indicate that there may be a problem with the geometric input for your surfaces. In fact, if you load your model into Euclid, it will automatically resolve some geometric issues for you.

If you run your file on a computer without a GPU you will see an explicit warning message stating that the simulation will revert to using PolygonClipping. Some computers have an integrated GPU and not a dedicated graphics card. When I run your file on my computer (with an integrated GPU), I can tell that the simulation is utilizing the GPU (and runs considerably faster than PolygonClipping).

Finally, I will point out that you can drastically reduce the number of shading surfaces in your model. For example, for six-sided cube-shaped neighboring building, you typically only need to include walls that you can "see" between a heat transfer surfaces in your model and the sky. A flat roof of an enclosed space will never cast a shadow. Typically, one or two walls of a cube will never shade your model. Ideally, EnergyPlus would have a way to automatically detect these situations and ignore those surfaces when performing shading calculations, but that is not currently the case.