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I am using one Cyclone IV FPGA and utilize the remote update feature. The factory.sof goes into one address on the serial configuration device and the application.sof goes into a higher address on the serial configuration device.
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I haven't tried using the Altera tools for that, so cannot help, sorry.
Note that the EPCS devices are just serial (SPI) Flash. If you want to control the device programming, you can write a programmer easily enough. That would allow you to independently update and verify multiple images in the flash.
That feature might exist in the nios2-flash-programmer tool:
http://www.altera.com/literature/ug/ug_nios2_flash_programmer.pdf Cheers,
Dave
Honored Contributor
