Documentation/4.1/Developers/Tutorials/Debug Instructions

From Slicer Wiki
Revision as of 19:37, 18 May 2012 by Crmullins (talk | contribs)
Jump to: navigation, search
Home < Documentation < 4.1 < Developers < Tutorials < Debug Instructions


The executable Slicer application Slicer-Superbuild/Slicer-build/Slicer (or Slicer.exe) is the launcher of the real application binary Slicer-Superbuild/Slicer-build/bin/SlicerQT-real.


Analyze a segmentation fault

$ ulimit -c unlimited
$ ./Slicer
... make it crash
$ ./Slicer --gdb ./bin/SlicerQT-real
(gdb) core core
(gdb) backtrace

GDB debug with launch arguments

The Slicer app launcher provides options to start other programs with the Slicer environment settings.

  • --launch <executable> [<parameters>]: executes an arbitrary program. For example, Slicer --launch /usr/bin/gnome-terminal starts gnome-terminal (then run GDB directly on SlicerQT-real)
  • --gdb: runs GDB then executes SlicerQT-real from within the debugger environment.

GDB debug by attaching to running process [RECOMMENDED]

Run ./Slicer-build/Slicer

Now, run "ps -Afww | grep SlicerApp-real" and note the PID of this binary.

Now, run "gdb --pid $PIDABOVE"

An alternative to quickly obtain the PID -- Run Slicer with the following command line argument:

$ ./Slicer --attach-process

This will bring up a window with the PID before loading any modules, which is helpful for debugging the loading process.

In Ubuntu 10.10, Ubuntu introduced a patch to disallow ptracing of non-child processes by non-root users -ie. only a process which is a parent of another process can ptrace it for normal users. You can temporarily disable this restriction by:

$ echo 0 | sudo tee /proc/sys/kernel/yama/ptrace_scope

To permanently allow it to edit /etc/sysctl.d/10-ptrace.conf and change the line:

  • kernel.yama.ptrace_scope = 1

to read:

  • kernel.yama.ptrace_scope = 0


GDB debug by using exec-wrapper

An alternative approach is to use a wrapper script to emulate the functionality of the app launcher. This will allow you to use gdb or a gdb-controlling program such as an IDE, in order to interactively debug directly from GDB without attaching.

The general idea of the wrapper is to set all of the appropriate environment variables as they would be set by the app launcher. From SlicerLauncherSettings:

  • [LibraryPath] contents should be in LD_LIBRARY_PATH
  • [Paths] contents should be in PATH
  • [EnvironmentVariables] should each be set

See this example script

Now, start gdb and do the following:

(gdb) set exec-wrapper ./WrapSlicer4 
(gdb) exec-file ./bin/SlicerQT-real
(gdb) run

Since VTK and ITK include many multithreaded filters, by default you will see lots of messages like the following from gdb during rendering and processing:

[New Thread 0x7fff8378f700 (LWP 20510)]
[Thread 0x7fff8b0aa700 (LWP 20506) exited]

These can be turned off with this command:

set print thread-events off

GDB debug in CodeLite IDE

Linux debugging with CodeLite IDE


For VisualStudio it's also possible to run the IDE with the correct environment to debug slicer.

The launcher gets configured with a special --VisualStudio option for this purpose.

Note that because CMake re-creates the solution file from within the build process, visual studio will sometimes need to stop and reload the project, requiring manual button pressing on your part. To avoid this, you can use a script to kick off the build and then re-start the IDE.

If you use cygwin, you can create simple shell scripts, for example in /usr/local/bin, which these several steps at once when run from the Slicer4-superbuild directory:

  • s4build (slicer4 build)
(cd Slicer-build; cmake.exe -VV --debug-output . && ./Slicer.exe --VisualStudio Slicer.sln /out buildlog.txt /build)
(cd Slicer-build; ./Slicer.exe --VisualStudio Slicer.sln)
  • s4sbuild (slicer4 super build)
(cmake.exe -VV --debug-output . && ./Slicer-build/Slicer.exe --VisualStudio Slicer.sln /out buildlog.txt /build)
(cd Slicer-build; ./Slicer.exe --VisualStudio Slicer.sln)

The s4build command re-runs cmake and then runs the build of Slicer only. When this completes, it launches visual studio with slicer loaded for debugging.

s4sbuild is similar, but it runs the superbuild process so that all the dependency libraries are updated. This takes longer, but is sometimes needed when there has been a change to CTK or other tools.

Note the buildlog.txt files for checking if anything went wrong.

Debugging a Test

Once VisualStudio is open with the Slicer environment loaded, it is possible to run and debug tests. To run all tests, build the RUN_TESTS project.

  1. To debug a test, find its project:
    1. Libs/MRML/Core tests are in the MRMLCoreCxxTests project
    2. CLI tests are in CLI_NAMETest project (e.g. ThresholdScalarVolumeTest)
    3. Loadable module tests are in qSlicerLOADABLE_NAMECxxTests project (e.g. qSlicerVolumeRenderingCxxTests)
    4. Module logic tests are in MODULE_NAMELogicCxxTests project (e.g. VolumeRenderingLogicCxxTests)
    5. Module widgets tests are in MODULE_NAMEWidgetsCxxTests project (e.g. VolumesWidgetsCxxTests)
  2. Go to the project debugging properties (right click -> Properties, then Configuration Properties/Debugging)
  3. In Command Arguments, type the name of the test (e.g. vtkMRMLSceneImportTest for project MRMLCoreCxxTests)
  4. If the test takes argument(s), enter the argument(s) after the test name in Command Arguments (e.g. vtkMRMLSceneImportTest C:\Path\To\Slicer4\Libs\MRML\Core\Testing\vol_and_cube.mrml)
    1. You can see what arguments are passed by the dashboards by looking at the test details in CDash.
    2. Most VTK and Qt tests support the -I argument, it allows the test to be run in "interactive" mode. It doesn't exit at the end of the test.
  5. Make the project Set As StartUp Project
  6. Start Debugging (F5)