Ok, first of all, you have gdb version 6.3.50
<< TCmdLineDebugger.ReadLn "~"GNU gdb 6.3.50.20050815-cvs (Thu Aug 27 13:01:51 UTC 2015)\n""
<< TCmdLineDebugger.ReadLn "~"Copyright 2004 Free Software Foundation, Inc.\n""
<< TCmdLineDebugger.ReadLn "~"GDB is free software, covered by the GNU General Public License, and you
This is ok, and supported by the IDE. This is the version that apple used to ship with xcode in the past.
I wonder, since you build from macports, if that is the version you wanted. MacPorts should have a later version. (gdb 7.8 or 7.9, maybe even 7.10).
Ensure you have the correct path. IIRC MacPorts installs the gdb binary somewhere deep in /opt/ or /opts/
That said, it should work with 6.3.50.
But with 6.3.50 timeouts are normal. The warning can be disabled in the debugger options (look through the property grid, on the "general" page (menu: tools > options > debugger)
There you can also reduce the timeout to 50 msec. (50 is the smallest allowed value greater than zero / zero will hang the debugger / 50 is safe).
From the rest of the logfile.
It looks like (after lots of timeouts) your app get started correctly.
It also looks like you have no breakpoints set, and there are no exceptions thrown in your app, and your app terminates normally.
Is this correct? (If so disable the warnings, and you may be fine)
If your app is a console app, then there is another issue, as this is not fully supported:
http://wiki.lazarus.freepascal.org/Debugger_Console_App#Mac
I also see from the log, that you use "dwarf" (project options / debug)
This is fine. However (IIRC, not sure, but you may want to try) with 6.3.50, using stabs might be better. If so, you need to do that for all packages too. (or use additions and overrides). So changing this might be a bit complicated.
So unless you get problems inspecting variables, then leave it at dwarf.
With newer gdb dwarf is ok, or even the only option.
Be aware, neither dwarf nor stabs will solve properties. Read
http://wiki.lazarus.freepascal.org/GDB_Debugger_Tips#Inspecting_data_types_.28Watch.2FHint.29