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Long time ago, Altera FPGA based boards could be designed in a way that the same PCB could support multiple footprints. Is this something that Altera dropped and no longer supports?
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I vaguely recall someone (perhaps Altera) having BGA footprints that were able to take different pin counts, but I have not seen this lately, so you can assume it is gone.
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We are designing a board that would benefit from this function a lot so we can deliver a low end and a high end design using the same PCB with alternative FPGA (choosing between F256, F484 and/or F672).
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Even on FPGAs with the same BGA pin count, there are pins that are inconsistent. For a design I did for the Stratix II EP2S60/90/130 FPGAs in 1020-pin packages, I first had to make a spreadsheet of all 1020 pins, and then enter the pin function for each package type, then where there was a mismatch, decide whether to just mark the pin as a no-connect, or make sure there was a stuff resistor option, eg. for VREF pins that must be tied to ground or VCC. The stuff resistor options need a via on one of the pins next to the BGA pad that needs to be tied to VCC or GND, so you need to 'reserve' some I/O pins that become the location of a via.
Altera has spreadsheets of the pin functions, its just that they're not necessarily in the format or order you want. I wrote Tcl scripts to read their spreadsheets and reformat them, so its not too much of a pain to reformat the tables.
Cheers,
Dave