Hi Scott,
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I've been using the Transceiver Toolkit with 14.0.0 build 200 in AVGZ and haven't seen any of the issues you're describing. While Altera hasn't updated the toolkit example designs in a while, you actually don't need any of the adapters anymore. In my Qsys system, I've got the tx and rx clock and data hooked up directly to the generator and checker blocks. I'm curious if that's causing the issues you're seeing with the auto detect? They appear as I'd expect when I launch the toolkit.
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I'm pretty sure the failed auto-setup was with the examples provided for the TTK ... perhaps for the Stratix IV Development Kit (since I have one of those).
The Arria V GZ that I am using is on the Texas Instruments TSW14J56 development kit, so I had to modify the TTK examples to support that kit. I think that failed too. I've got some notes around here that I need to turn into a PDF :)
I recall one of the issues being that the GUI would show the channels correctly, but would not allow you to change the pattern generator/checker patterns.
To compound the difficulty with using the TTK, the Native PHY setup I needed for my tests is not supported by the Qsys Custom PHY IP (or whatever its called), so I needed to create my Qsys system with the pattern generator and checker, but no PHY interface that was recognizable by the TTK. In this case, its still possible to use the TTK for eye-pattern sweeps etc (via the Reconfig controller), but the loopback checkbox does not work (I have a separate register to turn that on).
A lot of the TTK PHY components are not officially supported. Eg., if you try to create an instance of a core used in the examples, that core does not exist in the Qsys components menu. If you look in the _hw.tcl file for the components used in the example, their visibility is set to FALSE. You have to change that to TRUE and regenerate the .ipx file in the Quartus installation to make it visible. At that point, you can create a new Qsys system and add the various PHY IP components. Without changing the visibility, you can only copy-and-paste an existing Qsys system to create a new system.
TTK is nice, but its hardly a "completed" product :)
Cheers,
Dave