Nothing at 100% so where's the bottleneck?
I'm screwing around in Digital Devil Saga and noticed that when MTVU hack is on it lowers the EE usage from 100% to 75%, so naturally I assumed my GPU was the bottleneck at that point - but it's only at half load, and when I OC'd pretty heavily the FPS remained the same.

So neither EE, GS, VU, nor GPU are at 100%, what gives? Did MTVU hack just screw up the readings? I know enabling it lowered the FPS from 73 to 68 and coincidentally the i7's turbo speed went from 3.2ghz to 3.1 with MTVU enabled (even though 3.2ghz is the quad boost speed!)

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Usually when nothing is at 100% it's the GS that's the bottleneck. Check out your graphic's card VRAM usage, it might be full and that will cause it to be the bottleneck without having 100% power easy test would be reducing the internal resolution you are using significantly and checking out if that gives any kind of FPS boost
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Putting the laptop in performance mode at the Power Management settings (Windows Control Panel) while playing PCSX2 may aleviate or eliminate the issue there. Yours do not resemble the commonly seen symptom of the related issue but is something you should try before anything else.

Keep an eye on the temperature, if it gets too high you should seek for someway to improve the air flow.
Imagination is where we are truly real
The reading on the GS isn't 100% accurate. Sometimes I get high 90's - 100% on the GS, but when I look at GPU-Z, the amount the 3GB of vram weren't all used up. However, I do see some scenes of ZOE 2 goes up to 2.5GB.
The GS percentage is not only the usage of your GFX card.
It's mostly the GS emulation core on the second thread (MTGS) which converts the GS calls into DirectX calls.

Main Rig: i7-3770k @4.5ghz | 16GB DDR3 | Nvidia GTX 980 TI | Win 10 X64
Laptop: MSI GT62VR | i7-6700HQ | 16GB DDR4 | Nvidia GTX 1060 | Win 10 X64


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