The memory controller on X58 platform is integrated into the cpu itself, not in the motherboard. So I infer there should have a documentation telling the limitations regarding to ram quantity, frequencies and latencies the integrated memory controller into the Intel i7 900 series are able to handle.
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The Intel memory specs you quoted for the X58 platform (really the i7-900 series CPUs IMC, as you pointed out) are very conservative, and are really what Intel guarantees will work. In actual use, the CPU's IMC is much more capable than the specs would indicate. Since the the X58 platform is a triple channel memory system, one 1600 XMP DIMM in each channel fits the spec, regardless of the capacity of the DIMM, of course limited by the maximum amount of memory the platform supports.
I use six 2GB XMP 1600 DIMMs in my X58 board, and it works just fine at 1600. That is two XMP 1600 DIMMs per channel, for the same capacity per channel as your 4GB DIMMs. Some users use higher speed memory on this platform, so you should be fine.
Actually I also use six 2GB XMP DIMMs, but I downclock the frequency to 1333MHz. I have asked about 12GB RAM (3x4GB) at 1600Mhz, because I was considering an upgrade, so that I could use 12GB at 1600NHz.
Like you, I know many people populating all DIMMs with 2GB at 1600MHz, but as you said it is two XMP per channel, while Intel says "X.M.P. DIMMs and DDR3 1600 are supported for one DIMM per channel only".
That´s the point of my question, I mean is it fine to use two XMP 1600MHz DIMMs per channel then?
Yes, I'm doing it now on my X58 board, and have done so for over a year. I have six 2GB DIMMs running at 1600. The default speed is 1333 of course, but I use the XMP profile at 1600, at 1.5V, done.
Intel may have kept the memory speed spec low due to the "missing memory" issue, are you familiar with that? No, not the 32 bit OS thing. That is, you put in say 16GB, and the OS only sees 12GB, for example. Very common issue on X58 boards, you'll see it all over mother board forums. I've had it myself, but fixed it long ago. The IMC in the CPU is the issue IMO, and a tweak of it's voltage, either up or down (down worked in my case) is the main fix, IMO. Just FYI if you've never experienced it.
I've noticed over the years of the evolution of Intel's CPUs, that each new generation is more picky about the memory used with it. Builders in the past would just swap their DIMMs from one board to another, as long as they were the same type (DDR2, etc) they would work fine. After socket 775 CPUs, things changed IME. I only use memory on the mother boards QVL list, even if the memory manufacture claims that a product will work on 1366/X58 platforms, for example. Another FYI regarding memory and having it function correctly.
What are you concerned about happening if you use all your memory at 1600? BSOD, or no boot?
When I got a second 6GB Kit (3x2) to make it 12GB, I asked the memory manufacturer what I should do, apart from populating all DIMMs. The Patriot (manufacturer) said I should downclok it to 1333MHz on a 12GB config. Since then I use them that way, but I always wiondered about having it runing at 1600MHz.
I'm surprised the manufacture would say that, but not a big deal. The worst that can happen if you run all your memory at 1600 is the PC won't boot up, or Windows will blue screen, and the PC will restart over and over. Nothing will be damaged, and if you can't get into your BIOS to reset the memory, you just clear the BIOS. People that over clock CPUs and memory keep increasing their speed until the PC won't boot anymore or will blue screen (a fatal Windows error) and then turn it down a notch. But nothing is damaged due to a memory speed setting.