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I love to learn new things!
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Great! With FPGAs, there are plenty of opportunities.
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1. I do use the Eclipse ISE but I don't know how to use a debugger. Is there a tutorial or a document I could read to learn that?
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Altera has a "My First NIOS II Tutorial" that provides a walk-through of their Eclipse setup.
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2. I don't use an Avalon-MM bridge in Qsys. I've read papers about that but it seemed complicated and I preferred the self-made method to use a dual-port memory to access it both with software and with hardware.
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You can use self-made hardware, but its much more efficient if you create those self-made components as Qsys components and then wire them together in the Qsys GUI as this saves you having to create arbitration logic. Here some tutorials on using the JTAG interface to access custom logic;
http://www.alterawiki.com/wiki/using_the_usb-blaster_as_an_sopc/qsys_avalon-mm_master_tutorial http://www.ovro.caltech.edu/~dwh/correlator/pdf/altera_jtag_to_avalon_analysis.pdf http://www.ovro.caltech.edu/~dwh/correlator/pdf/vjtag.pdf --- Quote Start ---
3. I know Modelsim but I don't know how to do that.
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You need to learn this too. The best way to debug hardware issues is to trace the problem using SignalTap II and then reproduce that problem in simulation, and then debug in the simulator.
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If one of the 3 options seems better for you, please tell me and surely I'll need your help to go further...
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You need to learn them all :)
Cheers,
Dave