It seems the cooler on the Gigabyte does not push air out of the case so will that be a problem?
I have Coolermaster 690
Intake fans: 3, one front, two side.
Outake fans: 2, one back, one top (I could add another one on top)
i always buy "Custom" cooler over reference to have a cooler GPU but it's just a preference, (have a antec 900 and a directcu 2 gtx560...) i don't have any heat problem with that config so i think you shouldn't have too with your case...
As far as i know reference cooler runs hotter than custom but expulse heat out of the case so it's mainly a preference choice...
The Gigabyte one will be a bit quieter and possibly cool better. But, I have not been all that impressed with Gigabyte's coolers. I like the MSI Twin Frozer series a lot more. But I am running reference 680's, so...
A well ventilated case will not see issues with GPU coolers that vent to the interior. However, if you are running a small mini-tower or other case that has little airflow, this may become an issue.
I've got a machine I call my space heater that can't vent well, and under heavy load the case hits 50°C (on the outside temp, like where you can put your hand). Fortunately it is currently tasked as a server and even the extreme interior temp (75°C plus measured at the CPU) doesn't affect performance, but this is on the list to be replaced with a GPU-free solution.
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