So what exactly is the purpose of powering down FPGAs? If this was my mining rig, I'd be running it at 100% at all times. I see you mentioned temperature sensor - so maybe in places without adequate cooling or if a cooling system breaks you might want to turn things off... again I think I need to see a bit more of what you guys have designed so far.
It's for cases of having a network outage or your computer crashing, ...
The amount of FPGA space you will use for simple things like comm protocols is nearly negligible - especially when these modules are running at much reduced clock rates compared to the important stuff ( the hashing engine ). Another thing to think about - see what other FPGAs in the family have the same foot-print. A prototype board doesn't need to have the most expensive FPGA if a cheaper smaller FPGA can handle 1 hash engine, and this may help a little in the first round of prototyping.
A prototype board needs at least the XC6SLX75, because of the housing and because of the way you need to roll the miner up to fit inside. And the price difference to the 150 is small enough compared to the constant board costs (power supply, ...) that I would suggest going full hog on the first try. Maybe not both FPGAs, but at least the correct size.
I guess if the MCU is very cheap it's not that much of a hit to have one... but you are adding one more layer of complexity to the design. PC <==> USB chip <==> MCU <==> FPGA. And the MCU itself will need to have code written for it... I guess it matters what you really want the MCU to be able to accomplish. Or what you think the MCU may be able to accomplish in the long run.
The MCU is the USB chip, so there is no overhead there. The main ideas for not putting interface logic into the FPGA: the debugging is easier for non-HDL specialists, the FPGA can be brought up without needing a programmer cable (which hobbyists may not have!), the MCU can run on a different power rail than the FPGA and power up and down the FPGA, it can act as a brownout detector and temperature guard, there is no need for a dedicated USB chip when using a suitable MCU.
I think I need a bit more info on what the high level design architecture is going to be. How does the backplane/motherboard fit into this if each DIMM module has it's own MCU and USB controller? I would imagine ideally you would put these type of comm things onto the backplane/mobo itself - but I understand in terms of prototyping and development it'd be easier to have it on the module itself so you wouldn't need a backplane to debug/develop with it.
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Hybrid design: reduces entry level investment because you don't need the backplane for your first DIMM and the cost for the extra MCU, Mini-USB and Molex connectors together is small compared to the DIMM cost.