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Development boards use jumpers or dip switches.
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I've successfully driven MSEL pins, on Cyclone IV, from a micro. Indeed we have a shipping product that does just that. This followed previous work doing the same thing on a proprietary Cyclone II development platform. Make sure you have control over nCONFIG too so that you can ensure the MSEL sttings are stable when nCONFIG is released - when the MSEL pins are sampled. Don't try and use fast POR - there's no point.
There is one large caveat with this - it's not supported. As you pointed out, the datasheet states they should be tied directly to GND of VCCA and specifically states "
do not drive the msel pins with a microprocessor or another device". As Galfonz points out, jumpers/dip switches achieve this, the micro doesn't. Altera are unlikely to support you should not comply with the datasheet. However, with our shipping product we took the decision - following extensive testing that showed no failures - that the risk was low. 5 years and a large number of units later we have not seen any issues. My fingers remain crossed...
Cheers,
Alex
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Thanks alot both of you!