Debugging¶

Gdb¶

To attach gdb to a program currently running:

gdb --pid <pid>

The program is stopped after loading in gdb, use the command cont to make it go on.

To run a program with the debugger:

gdb <program>
run <args>

If the program terminates with an error, it is possible to get the backtrace of the stack with the command bt.

To put a breakpoint in a source file, use the following gdb command:

breakpoint <source file>:<line number>

The program stops when the breakpoint is reached and it is possible to execute step by step using the commands step and next. It is also possible to print a variable value with print <var>.

On Windows¶

• gdb on msys requires PYTHONPATH to point to the main $PYTHONHOME/Lib directory:
  

  export PYTHONPATH="$PYTHONPATH:$PYTHONHOME/Lib"

• then gdb anatomist will start, but python paths will be messed-up: it will not be able to load python modules (cannot import numpy, typically)
• the solution is to run anatomist "normally", then attach gdb on it
• for this we have to get the process id of the program to be debugged
  • open procmon (process monitor) with admin rights (important!), by right-clicking on the procmon icon and selecting "execute as administrator"
  • fill in admin login/passwd (.\admin-local for our VM)
  • in procmon, select the menu "Tools/process tree"
  • close the tree "wininit" if needed, and look for the process you need (inside a shell somewhere), note its PID.
• then run gdb --pid <pid>

• Stopping a program that hangs using Ctrl-C does not work: it closes gdb also...
• see: http://www.mingw.org/wiki/Workaround_for_GDB_Ctrl_C_Interrupt
• this program is compiled on our machine in /c/bv_issues/debugbreak/debugbreak.exe
• while the process is running and attached to gdb, using "debugbreak <pid>" will stop it and let gdb control it

Valgrind¶

This tool enables to track memory problems: invalid use of the memory, memory leaks...

To debug a program with Valgrind:

valgrind -v --show-reachable=yes --num-callers=20 --leak-check=full --tool=memcheck '<program>' >& /tmp/valgrind.log

In this example, the results of the Valgring analysis will be stored in the file /tmp/valgrind.log.