Hardware Debugging ccimx6ulsbc

Is there any way to do hardware debugging on my Digi Module ccimx6ulsbc on an embedded Linux?
Unfortunately the gdb server works with the Eclipse software
debugger and it behaves differently than when I run the application directly on the hardware without the debugger.

you can probably use JTAG, but JTAG debugging in Linux is not trivial. Have you tried printing out debug info to console or log file?