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I'm wondering what kind of redundancy I can put in place for the Freenas install itself. If the drive that Freenas is installed on fails, does that mean all my raid volumes are gone since its all software based?

I think my motherboard has a raid controller on it. I could make a raid 1, and install freenas on that. What if my motherboard dies, would that raid 1 volume be gone?

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RAID arrays - both in software and hardware - can be transplanted into a different server chassis. My experience has been primarily between identical servers (motherboards, etc dying on a production box and the drives being moved to a dev box).

The one caveat I have found - not directly related to your question as it pertains to hardware raid - is the second server should have the same RAID controller.

You also do need to be exceedingly careful to place the drives into the exact same slots / channels in the motherboard. I made that mistake at one point and nuked an otherwise working test system.

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