Is there a preferred pci-e lot to place a single GPU in? I have a MSI 890FX board (http://www.dvhardware.net/news/msi_890fx_gd70_coolaler.jpg) with a Sapphire Vapor-X 5850 card. I currently have the card towards the bottom of the board for 2 reasons. 1, I was concerned about creating a hotspot on the board by having the GPU, CPU and Memory all in a concentrated area. 2) The poser in me loved the slick look of the black motherboard and wanted to leave most of it visible. A friend just pointed out to me that it is not good for airflow to the card to have it near the bottom especially considering I have a bottom mounted PSU with a top fan. Even though this is all inside an Antec 1200 with a front case fan blowing in front of the GPU, is it best to move the card up a few slots?
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Typically the preferred slot for a single graphics card is the slot closest to the processor.
You might also want to check what the motherboard manual recommends.
eVGA and all the Gigabyte manuals that I have seen recommend using the slot closest to the CPU.