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Question : How the Nios manage the data transfert to the isp ? they are not on the same clock domain : the isp is 12 MHz and my Nios is 120MHz ?
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The NIOS example design uses several clock domains on the Avalon bus. This is said to speed up the design greatly.
You can use an Avalon bus bridge to cross a clock domain. The avalon bus at the other site of the bridge will be connected to the I/O pins with a standard appropriate bus I/O or with your own Avalon slave design.
-Michael