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Petalinux doesn't seem to come with useful tools like pstack or a full gdb, but it does include the gdbserver for remote debugging

This of course requires one to include debugging symbols in the executable.

Petalinux side

On the zynq, get the program's PID and do the following:

# gdbserver --attach <remote IP>:<port number> <pid>

Desktop linux side

Once the zynq has the gdbserver running, you run gdb on the host listed in the "gdbserver" command.

> source "/opt/Xilinx/SDK/"2015.4"/settings64.sh" && arm-xilinx-linux-gnueabi-gdb <path to local copy of zynq executable to debug>

Here the "source" command sets the environment needed to get the correct version of gdb. The executable file given has been compiled with the petalinux/Xilinx SDK compilers and is the same file running on the zynq.

Once you are in gdb, type the following to connect to the remote gdbserver

(gdb) target remote <zynq IP><port number>