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Newbie question (CCV5/Concerto/SYS_BIOS)

Other Parts Discussed in Thread: CONTROLSUITE

Hi,

I am new to TI/CSSV5/SYS_BIOS/Concerto and trying to learn more by create/debug a project. I have run in to some issues and hope someone could give some support.
I am using the TMDXDOCKH52C1 development board as target and planning to build an application that uses the quadrature decoder unit to read the motor velocity.

I have started a new Sys/Bios project and added the IQMath library.

First issue:
From examples I see uses of EQep1regs structure, how and what library/header file do I have to include to get access to this structures?

Second Issue:
I need to connect the motor encoder cable to the development board, what kind of inputs is routed to the quadrature module (programmable?)?
How do I set up the ports?

Third issue:
On the TMDXDOCKH52C1 development board it is to usb connectors (J2 and J20), I am planning to use the C2000 part of the Concerto, which one should I use when debugging/loading the software to the target?

Fourth issue:
How do I set up the clock on the TMDXDOCKH52C1 development board.

General issue:
Do I need to do more setup to run the project  (beside the application code)?