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I am using the original version of the Asus P9X79 Deluxe Motherboard.
Is it this board?
https://www.asus.com/Motherboards/P9X79_DELUXE/HelpDesk_CPU/
Are you using at least bios version 4502 ?
Check page 14 of 176 of the mobo manual (numbered xiv on the printed version)
It seems this mobo does have overclocking advanced features.
Most people that want to easily overclock buy K/X versions of CPUs which have unlocked multipliers.
Non K/X chips take more effort to overclock and you need to know what you are doing with vcore bclk etc.
Xeons can be overclocked just like the Intel 'Core i' range, but mobos need to allow it for non K/X chips.
Here's the manual
http://dlcdnet.asus.com/pub/ASUS/mb/LGA2011/P9X79-DELUXE/E8036_P9X79_DELUXE.pdf
Regarding your chip, was that a typo or is it an engineering sample as even Intel Ark doesn't list a chip for E5-2696 v2 @2.50GHz
http://ark.intel.com/products/family/78582/Intel-Xeon-Processor-E5-v2-Family
http://ark.intel.com/products/75281/Intel-Xeon-Processor-E5-2695-v2-30M-Cache-2_40-GHz
If it is correct then the base freq is 2.50GHz but it should be max turbo 3.30GHz
If your Xeon in that mobo isn't even turboing higher than 2.50GHz eg to 3.20GHz, then I would suspect the mobo/bios isn't correctly recognising your chip.
Yes. I am using either 4701 or 4801, I forget which.
I did attempt to use the built in easy overclock features that comes with the motherboard but it barely did anything. I was not comfortable with manually adjusting vcore bclk etc. settings.
Yes it is an engineering sample. It was supposed to be an engineering sample for an E5-2697 v2 but it identifies instead as an E5-2696 v2.
I knew it would be a sample, nice rare collectable chip. Some people online pay crazy money for engineering samples.
Without dealing with the build 'hands on', I don't know what to tell you.
I will warn you though that if you go altering overclocking settings in the BIOS eg bclk and vcore without learning and understanding how to overclock and the many risks, you can very easliy trash your system.
This whole thread subject really is off topic here but I will answer your on topic initial question:
CPUCores won't do anything regarding increasing your CPU clock speed or overclocking your CPU - it just doesnt work like that nor does it try to.
I guess if I were you I would maybe try some VR demos on Steam and see what your CPU clock speed is actually at in Task Manager. Chances are that this rare chip of yours is already doing a great job and may in fact be turboing correctly up to around 3.2GHz
If it isn't and you still aren't happy with the speed and want more, you will either need to learn about overclocking or simply sell/swap the chip for another high clock chip / a chip with an unlocked multiplier / or an i7 with higher clock/unlocked multiplier.
Depending how much people bid on this rare chip if you sold it, you could end up getting such silly money for it that the proceeds may amount to enough to build a current 7th gen intel chip system.... who knows!