Is gdb from the terminal outputting some kind of error or message?
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$ gdb
(gdb) break /.../ns-allinone-3.26/ns-3.26/scratch/test.cc:2494
No symbol table is loaded. Use the "file" command.
Make breakpoint pending on future shared library load? (y or [n]) y
Breakpoint 1 (/.../ns-allinone-3.26/ns-3.26/scratch/test.cc:2494) pending.
(gdb) run
Starting program: /.../ns-allinone-3.26/ns-3.26/build/scratch/test
[New Thread 0x2203 of process 36870]
GDB is clearly telling you that no symbol table is loaded. Make sure that you’re building ns3 in debug mode. Once that is done, use the command ./waf shell before running gdb because that will set the necessary environment variables for ns3 to run. If that works, check what environments the ./waf shell command is setting and replicate them.