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Is there a way to measure the performance of my Nios II implemented design?

Nios II

Yes.

If you select Library => Peripherals from SOPC Builder / Qsys, you will find the Performance Counter Unit. This peripheral can be used to measure the time of a specified section of code with the accuracy of the system clock.

Performance Counter has two counters internally.

* Time Counter: Measured with system clock accuracy for the execution time of the code section specified by the 64-bit counter
* Event Counter: A 32-bit counter measures the number of executions of a specified code section


For details, please refer to the document at the following URL, item Performance Counter Core.
  https://www.altera.com/en_US/pdfs/literature/ug/ug_embedded_ip.pdf


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