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If you see jumps in clockrate it is either due to dynamic underclocking (intel speedstep, overheating, power saving feature,...) or overclocking (turbo).
You should check which of these is the origin.
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SO3 speeds depends on the CRC hack level. You need at least full.
Anyway I was thinking about the speed comparison between "none" and "basic". I would need to check the rendering of the game. Maybe the GPU code is quite taxing or (much likely) it draws lots of triangle with a special fbmask.
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I believe both games use a similar stencil routine. In SO3 we have a crc hack for it, XS doesn't have one.
Check the shadows in XS in the 3rd screenshot vs SO3 doing the same with crc hacks disabled.
XS is also pushing many triangles in most of its scenes. It needs a lot of tweaking and most effects disabled to get any speed.
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Intel speedstep & intel turbo in bios?
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SO3 uses a special stencil that requires to transfer texture several times. It is killer for performance because you need to wait the transfer. GS will be idle in this time (low %).
I need to check XS. I vaguely remember somethings about a bit mask (accurate blending). Current implement requires to have in-order primitive to implement the effect properly and to flush GPU cache for every access. It is killer if you have more than 100 primitives. Most of the time, bit mask are used with sprite (nearly free with current algo). A couple of games use a hell ***** of triangles.