Please help to understand how Pcie works for ssd.
There's two kinds of pci-e lanes:
1. PCI-e 2.0 uses lanes that have a maximum speed of 500 MB/s
2. PCI-e 3.0 uses lanes that have a maximum of 970 MB/s
M.2 SSDs can use up to 4 pci-e lanes to communicate with the PC. It's UP TO because some SSD controllers are designed to use maximum 2 pci-e lanes because it makes the controller chip cheaper.
Also, by design, all M.2 SSDs will work with less lanes than they were designed to, so for example, a pci-e x4 M.2 SSD would also work with 2 lanes, or with 1 lane.
The two red pci-e slots are connected directly to the processor.
The Z97 chipset creates a bunch of pci-e 2.0 pci-e lanes, and these are connected to the pci-e x1 slots and to that M.2 connector.
On this motherboard, those pci-e lanes are connected to the 3 pci-e x1 slots, the pci-e x4 slot and the M.2 connector.
The M.2 connector receives 2 pci-e 2.0 lanes from the chipset, which means the M.2 connector can do up to 2 x 500 MB/s in both directions.
If you insert a M.2 SSD into that connector, because there aren't enough pci-e lanes created by the chipset, one of the pci-e x1 slots is turned off (its pci-e x1 lane is redirected to the M.2 connector) and the black pci-e x16 connector that's normally pci-e x4 either becomes x1 or x2, or becomes disabled as well. Simply put, the Z97 chipset doesn't create enough pci-e 2.0 lanes to give lanes to all slots at the same time.
Now, if you want more speed, one of the options you have is to buy a pci-e x4 to M.2 adapter card, like this one for example:
M.2 NGFF to Desktop PCIe x4 x8 x16 NVMe SATA Dual SSD PCI Express Adapter Card
Pci-E X4 To M.2 Ngff M/B Key Ssd Sata Adapter Converter Card For Desktop Pc E9H2
(only bottom m.2 is nvme,using pci-e, the top connector is like a bonus, allowing you to insert a SATA only m.2 SSD there and then connect it to PC using a regular SATA cable)
So, if you leave the original M.2 connector unused, and you leave that pci-e x1 slot that shares lanes with pci-e x4 slot unused, you'll have the black pci-e x16 slot with the maximum number of pci-e 2.0 lanes possible, which is 4.
Using that adapter card, your M.2 SSD will use 4 pci-e lanes, but they'll be pci-e 2.0 lanes, which means the maximum speed will be 4 x 500 MB/s in both directions.
Now, the two red pci-e x16 slots receives pci-e lanes from the CPU. Both can do 16 pci-e 3.0 lanes, but if you have two cards or two devices in the slots, each slot receives 8 pci-e 3.0 lanes from the CPU.
So if you install just one video card in one of the slots (shouldn't matter which one), that video card will run at pci-e x16 speed.
IF you install a second video card or any device (ex a 10gbit network card), the slots automatically become pci-e 3.0 x8
So what you could do, is take that pci-e to M.2 adapter card I linked above and insert it in one of those red pci-e slots.
Then, your video card will automatically run at pci-e 3.0 x8 speed (half) and the pci-e to M.2 adapter card will receive 8 pci-e 3.0 lanes but will only use 4 pci-e 3.0 lanes, because that's the maximum the M.2 connector supports.
It means your M.2 SSD will have up to 4 x 970 MB/s speed in both directions.
This would be the fastest speed for a M.2 SSD you could have on your motherboard, but as you can see the downside is your video card will be a tiny bit slower because it will only have 8 pci-e lanes.
It's worth noting that your bios may not recognize the M.2 SSD as a bootable drive if you insert it into those red pci-e x16 slots using an adapter card. It will work perfectly fine as storage drive, but may not be able to run windows from it. I'm not sure, your motherboard may be new enough that it will be detected just fine.
My advice would be to get one of those adapter cards but use the third pci-e x16 slot which only has 4 pci-e 2.0 lanes, giving the SSD up to 2 GB/s.
Your SSD can reach faster transfer speeds, but in real world very rarely you'll read or write files from your SSD at speeds higher than 1-2 GB/s, so you won't really feel the SSD as being slow.
However, if you use the adapter in the red slots, you're probably gonna feel something like 0.5-1% performance drop on the video card and it's not worth it.
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