Poor frame syncronisation causes screen flickering

[TakuikaNinja]

You are probably very aware of the screen flicker issue.
I had a look at this in Mesen2's event viewer and I can see why it has this problem. Your screen updates are frequently occurring outside of vertical blank. The PPU's VRAM can only be written to safely during blanking (vertical blank at the start of NMI, or forced blanking). During rendering, PPU accesses behave in an unpredictable manner as it is doing its own fetches to draw the screen.

Unfortunately, this seems to be a symptom of much bigger problem - Your program logic does not appear to be synchronised with PPU frames in any way. A more sensible approach on this system would be to implement a Main & NMI handler thread, as recommended by NESdev Wiki:

• https://www.nesdev.org/wiki/The_frame_and_NMIs
• https://www.nesdev.org/wiki/NMI_thread

[TakuikaNinja]

I had another look. Yeah, you're doing the PPU updates and keyboard reading using an IRQ hook system (based on the timer IRQ). That does not bode well with the strict vblank-driven nature of PPU accesses.

The advice hasn't changed - Keep the main logic at 60Hz, and buffer the PPU updates so they can be safely transferred by the NMI handler (and skipped on "lag frames"). There's no point in reading the keyboard more frequently than 60Hz either, so either put the polling routine at the start of the main loop, or do it in the NMI handler but skip it on "lag frames".

[decrazyo]

At the time, I decided to not use NMI to update the PPU during v-blank since LUnix allows application to register their own NMI handlers. It seemed preferable to make all of v-blank available to applications in case they needed it for some reason. In hindsight, that was probably a mistake. I'm not sure if any applications actually make use of that feature.
I agree that it's better to move that logic into the NMI handler.
I doubt that I'll get around to fixing it anytime soon but I'd accept a pull request if anyone wants to fix it.