Quartus Prime 16.1 crashes at very start of Assembler phase with NO ERROR MESSAGE

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1/ "However, those settings were still getting applied to my project" => make sure to check clear output directories checkbox in order to regenerate you IP files with the new options.

2/ I've tried to reproduce your issue. So I've generated an example design of Arria10 EMIF using quartus 16 pro and an I've added two additional clocks. The run was successful till assembling phase (which in contradiction with what you said).

could you give more details about your issue and the error returned by the assembler.

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1.) Yes, this is checked.

2.) Sounds like you reproduced my issue, where the assembler crashes after an otherwise successful compilation. I see no contradiction? I had to run the assembler from the command line to get any error output at all... GUI-driven compiles give the 3 lines of initial text output to the screen before silently falling over and asking you to describe what just happened. Sounds like this is what you've done, yes? So if you run the assembler from the command line on the failing project you'll get a bunch of red text that will explain exactly what the assembler is unhappy about. I'd have to re-break my project now to get this exact output for you... but much of it seemed like it was PLL parameter checks that were failing. What text does your failing project output from this operation? I'd be happy to confirm if it is similar to what I observed.

Cheers,

-VJR