What is a Qsys BFM?

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That point is clear, I understand that. The question is, when I create a Qsys system and then choose options to create BFM and a testbench with the simulation models and open modelsim and run msim_setup.tcl, in all this how does the BFM know what value it is supposed to put onto the component? Or do I have to add the BFM manually in the Qsys itself and otherwise they will not be added into the simulation model? How do I tell the BFM what it is supposed to do? I thought that the BFM just does things on its own. It has been created and it just works when we choose the BFM option in Qsys before we generate the system.

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Aside from some default initial processing, the BFM does not do anything. It is up to you to write a testbench which instructs the BFM to perform various tasks for you. Qsys simply instantiates the BFM entities with proper parameters and connects them to the design so they are ready to be useful to you.

This is explained in the previously linked ug_avalon_verification_ip.pdf but you might also enjoy the wikipedia definition of BFM and the linked articles from there: http://en.wikipedia.org/wiki/bus_functional_model

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Do 3rd part IP vendors need to produce BFM for thier IP as well, even if it shall integrate with a Analon-MM or any other known interface and not just be a conduit?

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A 3rd party IP vendor might use the BFM's in the construction of their own testbenches for verifying their IP components. Or they might use their own methods to accomplish the same goals.