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On the contrary, when the NIOS loads the firmware from the same flash it takes around 0.1 second.
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The firmware size is about 2.5MBytes so my calculation about the read speed during boot takes that into acount.
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The flash device I'm using is epcs128.
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2.5MB / 0.1s = 25MB/s
DCLK fMAX of EPCS128 during fast read is 40MHz (which is only 5MB/s if you ignore overhead).
So, something doesnt add up. Can you clarify?
Since you're already using SignalTap, configure it to capture the bootloader sequence and see if it is getting significantly better read timing than your runtime performance. This will simply indicate if you have a problem that you might slightly improve through software optimization.