Segmentation Fault vs libG4graphics?

AlexAerPhys · November 23, 2020, 11:40pm

Ubuntu 18.04 LTS (used through Windows WSL)
Geant4-10.6.p03
gcc 7.5.0

Hello,
I have followed the standard guidelines here for building and installing Geant4.
By the end of it, I have run the geant.sh and geant4make.sh scripts and my environmental variables are

aeroulis89@DESKTOP-J2QLNGA:~/g4B1example/build$ printenv | grep G4
G4UI_USE_TCSH=1
G4INCLDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/G4INCL1.0
G4INSTALL=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/geant4make
G4WORKDIR=/home/aeroulis89/geant4_workdir
G4LIB_USE_ZLIB=1
G4LEVELGAMMADATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/PhotonEvaporation5.5
G4RADIOACTIVEDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/RadioactiveDecay5.4
G4MULTITHREADED=1
G4PIIDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/G4PII1.3
G4SAIDXSDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/G4SAIDDATA2.0
G4ABLADATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/G4ABLA3.1
G4SYSTEM=Linux-g++
G4REALSURFACEDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/RealSurface2.1.1
G4INCLUDE=/home/aeroulis89/geant4.10.06.p03-install/include/Geant4
G4NEUTRONHPDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/G4NDL4.6
G4PARTICLEXSDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/G4PARTICLEXS2.1
G4LIB=/home/aeroulis89/geant4.10.06.p03-install/lib/Geant4-10.6.3
G4VIS_USE_OPENGLQT=1
G4ENSDFSTATEDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/G4ENSDFSTATE2.2
G4LEDATA=/home/aeroulis89/geant4.10.06.p03-install/share/Geant4-10.6.3/data/G4EMLOW7.9.1
G4UI_USE_QT=1
G4LIB_BUILD_SHARED=1

Then, I embark on trying out example B1:

cp -r geant4.10.06.p03-install/share/Geant4-10.6.3/examples/basic/B1 g4B1example
cd /home/g4B1example
mkdir build
cd build

aeroulis89@DESKTOP-J2QLNGA:~/g4B1example/build$ cmake -DGEANT4_DIR= /home/aeroulis89/geant4.10.06.p03-install/lib/Geant4-10.6.3/ /home/aeroulis89/g4B1example/
    -- The C compiler identification is GNU 7.5.0
    -- The CXX compiler identification is GNU 7.5.0
    -- Check for working C compiler: /usr/bin/cc
    -- Check for working C compiler: /usr/bin/cc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Detecting C compile features
    -- Detecting C compile features - done
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    -- Found EXPAT: /usr/lib/x86_64-linux-gnu/libexpat.so (found suitable version "2.2.5", minimum required is "2.2.5")
    -- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so
    -- Configuring done
    -- Generating done
    CMake Warning:
      Manually-specified variables were not used by the project:

    GEANT4_DIR
-- Build files have been written to: /home/aeroulis89/g4B1example/build

Then I do make

aeroulis89@DESKTOP-J2QLNGA:~/g4B1example/build$ make
Scanning dependencies of target exampleB1
[ 12%] Building CXX object CMakeFiles/exampleB1.dir/exampleB1.cc.o
[ 25%] Building CXX object CMakeFiles/exampleB1.dir/src/B1ActionInitialization.cc.o
[ 37%] Building CXX object CMakeFiles/exampleB1.dir/src/B1DetectorConstruction.cc.o
[ 50%] Building CXX object CMakeFiles/exampleB1.dir/src/B1EventAction.cc.o
[ 62%] Building CXX object CMakeFiles/exampleB1.dir/src/B1PrimaryGeneratorAction.cc.o
[ 75%] Building CXX object CMakeFiles/exampleB1.dir/src/B1RunAction.cc.o
[ 87%] Building CXX object CMakeFiles/exampleB1.dir/src/B1SteppingAction.cc.o
[100%] Linking CXX executable exampleB1
[100%] Built target exampleB1

Finally, I attempt to run it

aeroulis89@DESKTOP-J2QLNGA:~/g4B1example/build$ ./exampleB1
Available UI session types: [ Qt, GAG, tcsh, csh ]
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-aeroulis89'
G4WT1 > /control/saveHistory
G4WT0 > /control/saveHistory
G4WT1 > /run/verbose 2
G4WT0 > /run/verbose 2
G4WT1 > /run/initialize
G4WT0 > /run/initialize
G4WT0 > /run/physicsModified
G4WT1 > /run/physicsModified
Segmentation fault

I do not get a specific error number which is strange…
Then I try a naive idea, which tells me something about the libG4graphics library…

aeroulis89@DESKTOP-J2QLNGA:~/g4B1example/build$ sudo ./exampleB1
./exampleB1: error while loading shared libraries: libG4graphics_reps.so: cannot open shared object file: No such file or directory

However this library does exist…

aeroulis89@DESKTOP-J2QLNGA:~/g4B1example/build$ ldd exampleB1 | grep libG4graphics
        libG4graphics_reps.so => /home/aeroulis89/geant4.10.06.p03-install/lib/libG4graphics_reps.so (0x00007f06d4be1000)

As another clue that I saw might be useful to know from other similar forum questions is my LD_LIBRARY_PATH

aeroulis89@DESKTOP-J2QLNGA:~/g4B1example/build$ echo $LD_LIBRARY_PATH
/usr/lib/x86_64-linux-gnu:/home/aeroulis89/geant4.10.06.p03-install/lib:/home/aeroulis89/geant4.10.06.p03-install/lib:/home/aeroulis89/builddir/lib

Can someone help me debug this? Any hint would be much appreciated.
Alex

php1ic · November 24, 2020, 9:26am

I think it’s case sensitive when you run cmake, so you need to use -DGeant4_DIR and not -DGEANT4_DIR.

That is why you get the CMake Warning section of the ouput. Don’t know if the space after the equals matters, but I would also get rid of that.

AlexAerPhys · November 24, 2020, 11:11am

Thank you very much for that.
Indeed, after making these changes, the warning disappears

aeroulis89@DESKTOP-J2QLNGA:~/B1example/build$ cmake -DGeant4_DIR=/home/aeroulis89/geant4.10.06.p03-install/lib/Geant4-10.6.3/ /home/aeroulis89/B1example/B1/
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found EXPAT: /usr/lib/x86_64-linux-gnu/libexpat.so (found suitable version "2.2.5", minimum required is "2.2.5")
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so
-- Configuring done
-- Generating done
-- Build files have been written to: /home/aeroulis89/B1example/build

Unfortunately, the segmentation fault still persists though even with this change…

php1ic · November 24, 2020, 11:39am

Your install and setup look correct, can you run other UI applications through that instance of Linux?

I don’t have any experience with WSL, but a quick google suggests you need to have an X server running on your windows machine for Linux based UI programs to work.

AlexAerPhys · November 24, 2020, 12:23pm

Yes, I am setting up an X server so that I can open up UI programs from Linux. This has worked for me for different programs (firefox, gedit,…etc.)
If it is of any help, the command I have to run in order to “connect” Linux with the X server is
export DISPLAY=$(cat /etc/resolv.conf | grep nameserver | awk '{print $2}'):0 export LIBGL_ALWAYS_INDIRECT=1

Is there a log where I could check what sort of segmentation fault I get?

bmorgan · November 24, 2020, 12:27pm

I think (but I’ve not used WSL yet) that you should be able to use normal debugging tools like gdb to run and get a backtrace of the segfault. Geant4’s built in Release mode by default (but you can change to RelWithDebInfo, so won’t give line numbers, but this should at least identify the class/member function where it goes wrong.

AlexAerPhys · November 24, 2020, 7:11pm

Thank you both for taking the time to help.

I did run the executable with gdb and got the following

(gdb) run
Starting program: /home/aeroulis89/B1example/build/exampleB1
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Available UI session types: [ Qt, GAG, tcsh, csh ]
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-aeroulis89'
[New Thread 0x7fffe2589700 (LWP 1685)]
[New Thread 0x7fffe1032700 (LWP 1686)]
[New Thread 0x7fffe0809700 (LWP 1688)]
[New Thread 0x7fffd3fff700 (LWP 1689)]
G4WT1 > /control/saveHistory
G4WT0 > /control/saveHistory
G4WT1 > /run/verbose 2
G4WT0 > /run/verbose 2
G4WT1 > /run/initialize
G4WT0 > /run/initialize
G4WT1 > /run/physicsModified
G4WT0 > /run/physicsModified

Thread 1 "exampleB1" received signal SIGSEGV, Segmentation fault.
0x00007fffecf141e8 in QOpenGLContext::format() const () from /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5

any clue where that points to?
Alex

php1ic · November 25, 2020, 2:11pm

This is beyond me now, but running bt in gdb after the crash to get the full stack trace might be helpful.

AlexAerPhys · November 25, 2020, 4:02pm

Thanks for the backtrace command tip (I am not familiar with using gdb).

(gdb) bt
#0  0x00007fffecf141e8 in QOpenGLContext::format() const () from /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5
#1  0x00007fffecf14354 in QOpenGLContext::isOpenGLES() const () from /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5
#2  0x00007fffecf143b9 in QOpenGLContext::versionFunctions(QOpenGLVersionProfile const&) const ()
   from /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5
#3  0x00007fffedda6634 in ?? () from /usr/lib/x86_64-linux-gnu/libQt5OpenGL.so.5
#4  0x00007fffeddaa3b0 in QGLWidget::renderText(double, double, double, QString const&, QFont const&) ()
   from /usr/lib/x86_64-linux-gnu/libQt5OpenGL.so.5
#5  0x00007ffff70803b0 in G4OpenGLQtViewer::DrawText(G4Text const&) ()
   from /home/aeroulis89/geant4.10.06.p03-build/BuildProducts/lib/libG4OpenGL.so
#6  0x00007ffff705877b in G4OpenGLStoredSceneHandler::AddPrimitive(G4Text const&) ()
   from /home/aeroulis89/geant4.10.06.p03-build/BuildProducts/lib/libG4OpenGL.so
#7  0x00007ffff70557cc in G4OpenGLStoredViewer::AddPrimitiveForASingleFrame(G4Text const&) ()
   from /home/aeroulis89/geant4.10.06.p03-build/BuildProducts/lib/libG4OpenGL.so
#8  0x00007ffff7055bc6 in G4OpenGLStoredViewer::DrawDisplayLists() ()
   from /home/aeroulis89/geant4.10.06.p03-build/BuildProducts/lib/libG4OpenGL.so
#9  0x00007ffff7087a7e in G4OpenGLStoredQtViewer::ComputeView() ()
   from /home/aeroulis89/geant4.10.06.p03-build/BuildProducts/lib/libG4OpenGL.so
#10 0x00007ffff7087bfa in G4OpenGLStoredQtViewer::paintGL() ()
   from /home/aeroulis89/geant4.10.06.p03-build/BuildProducts/lib/libG4OpenGL.so
#11 0x00007fffedda9cc4 in QGLWidget::glDraw() () from /usr/lib/x86_64-linux-gnu/libQt5OpenGL.so.5
#12 0x00007fffed6d5048 in QWidget::event(QEvent*) () from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#13 0x00007fffed69683c in QApplicationPrivate::notify_helper(QObject*, QEvent*) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#14 0x00007fffed69e104 in QApplication::notify(QObject*, QEvent*) () from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#15 0x00007fffec9188d8 in QCoreApplication::notifyInternal2(QObject*, QEvent*) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
#16 0x00007fffed6ce19a in QWidgetPrivate::sendPaintEvent(QRegion const&) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#17 0x00007fffed6ce75a in QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, int, QPainter*, QWidgetBackingStore*) () from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#18 0x00007fffed6a3f5b in QWidgetPrivate::repaint_sys(QRegion const&) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#19 0x00007fffed6f1d4e in ?? () from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#20 0x00007fffed6f266d in ?? () from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#21 0x00007fffed69683c in QApplicationPrivate::notify_helper(QObject*, QEvent*) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#22 0x00007fffed69e104 in QApplication::notify(QObject*, QEvent*) () from /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5
#23 0x00007fffec9188d8 in QCoreApplication::notifyInternal2(QObject*, QEvent*) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
#24 0x00007fffecedb49f in QGuiApplicationPrivate::processExposeEvent(QWindowSystemInterfacePrivate::ExposeEvent*) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5
#25 0x00007fffecedc0dd in QGuiApplicationPrivate::processWindowSystemEvent(QWindowSystemInterfacePrivate::WindowSystemEvent*) () from /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5
#26 0x00007fffeceb32eb in QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5
#27 0x00007fffe6c97260 in ?? () from /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5
#28 0x00007fffea50f417 in g_main_context_dispatch () from /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
#29 0x00007fffea50f650 in ?? () from /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
#30 0x00007fffea50f6dc in g_main_context_iteration () from /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
#31 0x00007fffec97188f in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
#32 0x00007fffec91690a in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) ()
   from /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
#33 0x00007fffec91f9b4 in QCoreApplication::exec() () from /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
#34 0x00007ffff6ded6c4 in G4UIQt::SessionStart() ()
   from /home/aeroulis89/geant4.10.06.p03-build/BuildProducts/lib/libG4interfaces.so
#35 0x0000555555559a83 in main (argc=<optimized out>, argv=0x7fffffffd978)
    at /home/aeroulis89/B1example/B1/exampleB1.cc:103

I get a black window opened up but it crashes at the ui->SessionStart();
It seems to be a visualisation issue?
By the way, I noticed some “??” in frames #3, 19, 20, 27 and 29. Is that normal?

Alex

php1ic · November 25, 2020, 5:04pm

I think the “??” mean that you compiled geant4 in Release mode rather than RelWithDebInfo so some of the binaries don’t have debug symbols. See the CMAKE_BUILD_TYPE option during configuration.

Poking around a bit I found this post suggesting to disable LIBGL_ALWAYS_INDIRECT. From one of your comments above, you look to enable it. Have you tried that?

AlexAerPhys · November 25, 2020, 7:13pm

Magic! that worked for me! I can’t thank you more. I learnt quite a few things 2 days now.

To sum up, when launching VcXsrv from a GUI client, I had to leave the second option box “Native opengl” unchecked.

then, on a bash I would connect Linux to the X server by
export DISPLAY=$(cat /etc/resolv.conf | grep nameserver | awk '{print $2}'):0
and then I was able to run B1 example.

bmorgan · November 27, 2020, 4:58pm

Thanks both for the feedback and info - we don’t test/support WSL at the moment, so really useful to have this info

Sid91 · June 8, 2021, 12:42pm

Hi

sudo cmake -DCMAKE_INSTALL_PREFIX=…/GEANT4.10.07.p01 -DGEANT4_BUILD_MULTITHREADED=ON -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_QT=ON -DGEANT4_USE_RAYTRACER_X11=OFF -DGEANT4_USE_OPENGL_X11=ON -DGEANT4_USE_GDML=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo -DGEANT4_USE_XM=OFF -DGEANT4_ENABLE_TESTING=OFF -DGEANT4_BUILD_CXXSTD=14 -DGEANT4_USE_RAYTRACER_X11=OFF -DGEANT4_USE_SYSTEM_CLHEP=OFF -DGEANT4_USE_SYSTEM_ZLIB=OFF …/geant4.10.07.p01

Known Features:
staticlibs[no] multithreading[yes] smartstack[no] php_as_hp[no] clhep[yes] expat[no] zlib[yes] gdml[yes] usolids[no] freetype[no] hdf5[no] g3tog4[no] qt[yes] motif[no] raytracer-x11[no] opengl-x11[yes] openinventor[no]

I’m also trying to use geant4 with WSL2(ubnutu 20.04). For the example B2a, with 100 events it crashs and says to increase the “/vis/ogl/set/displayListLimit”. Once done, it works but the 3D view is verry lagged(low fps), is it normal ?

Otherwise it is clearly due to wsl drivers/opengl lib. By default examples use “OpenGLStoredQt”, do you know the difference between OpenGLStoredQt and OpenGLImmediateQt ?

I launched the example B2a with gdb, after typing “where” I get this if it can help :
Thread 1 “exampleB2a” received signal SIGINT, Interrupt.
0x00007ffff6d5faff in poll () from /usr/lib/x86_64-linux-gnu/libc.so.6
(gdb) where
#0 0x00007ffff6d5faff in poll () from /usr/lib/x86_64-linux-gnu/libc.so.6
#1 0x00007ffff2a8636e in ?? () from /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
#2 0x00007ffff2a864a3 in g_main_context_iteration ()
from /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
#3 0x00007ffff3e8d565 in QEventDispatcherGlib::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
#4 0x00007ffff3e344db in QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) ()
from /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
#5 0x00007ffff3e3c246 in QCoreApplication::exec() ()
from /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
#6 0x00007ffff7b90063 in G4UIQt::SessionStart (this=0x5555555ee130)
at /home/dz/products/geant4.10.07.p01/source/interfaces/basic/src/G4UIQt.cc:1922
#7 0x000055555555dd5b in main (argc=, argv=0x7fffffffd828)
at /home/dz/TEST/B2/B2a/exampleB2a.cc:98

Regards

Sid91 · June 8, 2021, 12:46pm

Also, for the option /run/numberOfThreads , it doesn’t work I get this message, you already faced this message?

illegal application state – command refused:"/run/numberOfThreads 8"

allison · June 9, 2021, 2:11pm

Hi

The second query first. Some commands can only be executed in certain application states. /run/numberOfThreads can only be executed in “PreInit” state, before run initialisation. Juts move it earlier. For example, in exampleB1 it is init_vis.mac.

John

allison · June 9, 2021, 2:20pm

Hi again

Now the first query. 100 B2 events have lots of particle tracks - I’d expect it to have a low fps.

The difference between OpenGLStoredQt and OpenGLImmediateQt is that the former uses a graphical database (OpenGL display lists) so that rotating and zooming, etc., is fast. The latter does not so for every new frame the image is re-generated from the Geant4 kernel objects (volumes and trajectories, etc.).

Re the crash, looks like you are in the Qt graphical event loop. I have noticed Qt sometimes crashes if you ask too much it. All I can suggest is, please try again, perhaps with just a few events to start with. If it persists, we’ll have another look.

John

Sid91 · June 9, 2021, 3:12pm

So if I’ve well understand, I type ./exampleB1 init_vis.mac. This input gives me this error, and no visualization :

# Use this open statement to create an OpenGL view: /vis/open OGL 600x600-0+0 /vis/sceneHandler/create OGL WARNING: G4VisCommandSceneHandlerCreate::SetNewValue: Using fallback graphics system: OpenGLStoredX (OGLSX) /vis/viewer/create ! ! 600x600-0+0 /vis/viewer/refresh #

I report it but I do not think there is a possible thing to do, this is related to wsl I think

priyanshu-gif · June 9, 2021, 3:23pm

Hi,
can you see this command line /vis/open OGL in your init_vis.mac
or to run example B1 simply write ./exampleB1
i think it should work. can you try this ?
Priyanshu

Sid91 · June 9, 2021, 3:42pm

Oh yes only “./exampleB1” it works, I have the qt vis but there is warnings(refer to the first message). And “./exampleB1 init_vis.mac” did not work at all

Regards

Sid91 · June 10, 2021, 11:47am

Sorry I was not understanding when you talked about the init_vis.mac, now I found it and there is no line with /vis/open OGL. I tried to add it with “OGLI”, does not work, it uses OGLS

I edited the file in the build folder of example

Regards