Debugging

1. Always check output for warnings using grep. Warnings like “can’t solve overlap” or “separation <0” often indicate a bug or a very dense system.

2. Rerun with the same seed to isolate the error: ./nerdss -f parms.inp -s 1234091

3. Run sample_inputs/VALIDATE_SUITE. Ensure it works on initial start (-f parms.inp) and on restart (-r restart.dat).

4. If you edited an include file, recompile clean by removing the obj directory to avoid segmentation faults.

5. Use debuggers like gdb, lldb, or valgrind:

1. Recompile all code with CFLAGS=-g and remove -O3.

2. Launch the debugger: lldb nerdss

3. Run the program: run -f parms.inp -s 123445

4. Use commands like bt (backtrace) and print myVariable to debug.

5. On macOS, use libgmalloc for strict memory tracking: env DYLD_INSERT_LIBRARIES=/usr/lib/libgmalloc.dylib

6. Use help [command] for assistance.

7. Set breakpoints with break file1.c:6 or break my_func.

8. Use step, next, watch my_var, backtrace, where, finish, delete, info breakpoints, stop, and other commands as needed.

9. For heap corruption issues, enable -fsanitize=address and reserve space in vectors.