I have this scene with a huge church with many small windows in it. What would be the best way to light it? A skydome with many small lightportals or a separate light for each window? It's hard to get a reasonable render time and a clean picture.
Separate area lights for each window is your best option. Skydome is way too slow and super grainy, even with Portals. However, it's very important that you apply a Decay Filter to each light, with Near Attenuation enabled. All Arnold lights use quadratic decay by default, which means that the geometry near the lights is going to be massively overexposed. Near Attenuation with a very high Near End value will even out the intensity over distance, so that the geometry at the other end of the space is illuminated approximately the same as the geometry near the light source.
It would be useful if you could share renders using both methods. How many diffuse/ light samples are you using? Adding some interior lighting might help with darkness/noise.
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