anatomist refuses to display my images

[Stephane_Sockeel]

Bonjour,

I have a little trouble with Anatomist, which stubbornly refuses to display my images.
I'm not against a little help from you to solve the problem.

here are some clues:

DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=12.04
DISTRIB_CODENAME=precise
DISTRIB_DESCRIPTION="Ubuntu 12.04.2 LTS"

00:00.0 Host bridge: Intel Corporation Ivy Bridge DRAM Controller (rev 09)
00:02.0 VGA compatible controller: Intel Corporation Ivy Bridge Graphics Controller (rev 09)
[...]

OpenGL vendor string: Intel Open Source Technology Center
OpenGL renderer string: Mesa DRI Intel(R) Ivybridge Desktop
OpenGL version string: 3.0 Mesa 9.0.2
OpenGL shading language version string: 1.30
OpenGL extensions:

And the error message from anatomist :

Fontconfig warning: "/etc/fonts/conf.d/11-lcd-filter-lcddefault.conf", line 9: invalid constant used : lcddefault
Fontconfig warning: "/etc/fonts/conf.d/53-monospace-lcd-filter.conf", line 17: invalid constant used : lcdlegacy
Starting Anatomist.....
config file : /home/ssockeel/.anatomist/config/settings.cfg
PyAnatomist Module present
global modules: /usr/local/brainvisa-4.3.0/share/anatomist-4.3/python_plugins
home modules: /home/ssockeel/.anatomist/python_plugins
loading module volumepalettes
loading module meshsplit
loading module gradientpalette
loading module selection
<H1>Anatomist launched</H1>
loading module paletteViewer
loading module anacontrolmenu
loading module palettecontrols
loading module bsa_proba
loading module histogram
loading module profilewindow
loading module modelGraphs
loading module foldsplit
all python modules loaded
Multitexturing present
Number of texture units: 8
GL_ARB_shadow present
GL_SGIX_shadow extension not available
GL_SGIX_depth_texture extension not available
GL_ARB_depth_texture extension present
GL_ARB_texture_cube_map extension present
GL_EXT_texture_cube_map extension present
Number of texture units: 8
Erreur de segmentation (core dumped)

if you need more, say it

Merci d'avance
Stéphane

[riviere]

Hi Stéphane,
Does the crash occur when opening an empty 3D window, or when putting an object in it ?
You can try disabling hardware 3D, to see if it makes any difference: edit your /etc/X11/xorg.conf (as root) and add a line

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      Option "NoAccel" "1"

in the Device section. Then restart the X server (or reboot).
If it still doesn't work, you may try running anatomist in gdb, and when it crashes, get a backtrace of the stack to see where it crashes.
Denis

[Stephane_Sockeel]

Does the crash occur when opening an empty 3D window, or when putting an object in it ?

Only when I put an object in the windows.

I'll try your method and come back to you.

[Stephane_Sockeel]

it still not working

I'm not familiar with gdb. How can I run anatomist with gdb ?

[riviere]

Does it occur with any type of object (mesh, volume) ?
I still think it's related to your system OpenGL implementation... I don't know if you can easily switch to a software-only OpenGL/Mesa implementation (to test).
For gdb (the debugger), you should
1. run the setup script to set all needed environment variables in your terminal, typically in bash shells:

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. <brainvisa>/bin/bv_env.sh

(this is needed here otherwise you would run gdb on the wrapper script, not on anatomist itself)
2. run gdb:

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gdb anatomist

3. inside gdb, run anatomist:

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run

4. use anatomist until it crashes
5. When it crashes, in gdb, get the stack info:

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bt

and tell us what it outputs.
It will only give clues on where in the program and libraries it crashes, we should see it it happens in OpenGL or in our code in anatomist.
6. quit gdb:

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quit

Denis

[Stephane_Sockeel]

it's weird, I've this error message when I try to start gdb :

. /usr/local/brainvisa-4.3.0/bin/bv_env.sh
gdb anatomist
ImportError: No module named site

[riviere]

Oh, I had never noticed that gdb is now linked with python (which can be very useful for other purposes, but not here...)
Then try not sourcing the bv_env.sh script, but running gdb thyis way:

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gdb --args <brainvisa>/bin/bv_env anatomist

(then proceed as in the previous message)
Denis

[Stephane_Sockeel]

Ok,here we are...

Program received signal SIGSEGV, Segmentation fault.
0x00007fffc5418ee2 in vbo_save_playback_vertex_list ()
from /usr/lib/x86_64-linux-gnu/libdricore9.0.3.so.1

#0 0x00007fffc5418ee2 in vbo_save_playback_vertex_list ()
from /usr/lib/x86_64-linux-gnu/libdricore9.0.3.so.1
#1 0x00007fffc5343592 in ?? ()
from /usr/lib/x86_64-linux-gnu/libdricore9.0.3.so.1
#2 0x00007fffc5346e39 in ?? ()
from /usr/lib/x86_64-linux-gnu/libdricore9.0.3.so.1
#3 0x00007fffc5347362 in _mesa_CallList ()
from /usr/lib/x86_64-linux-gnu/libdricore9.0.3.so.1
#4 0x00007ffff78756b4 in anatomist::GLWidgetManager::drawObjects(anatomist::GLWidgetManager::DrawMode) ()
from /usr/local/brainvisa-4.3.0/lib/libanatomist.so.4.3.0
#5 0x00007fffe0beac2d in vtkQAGLWidget::drawObjects(anatomist::GLWidgetManager::DrawMode) () from /usr/local/brainvisa-4.3.0/lib/libanavtk.so.4.3.0
#6 0x00007ffff7874cd0 in anatomist::GLWidgetManager::paintGL() ()
from /usr/local/brainvisa-4.3.0/lib/libanatomist.so.4.3.0
#7 0x00007ffff64d63fa in QGLWidget::glDraw() ()
from /usr/local/brainvisa-4.3.0/lib/libQtOpenGL.so.4
#8 0x00007fffe0beab9d in vtkQAGLWidget::updateGL() ()
from /usr/local/brainvisa-4.3.0/lib/libanavtk.so.4.3.0
#9 0x00007ffff78fe06b in AWindow3D::refreshNow() ()
from /usr/local/brainvisa-4.3.0/lib/libanatomist.so.4.3.0
#10 0x00007ffff787f808 in QAWindow::triggeredRefresh() ()
from /usr/local/brainvisa-4.3.0/lib/libanatomist.so.4.3.0
---Type <return> to continue, or q <return> to quit---
#11 0x00007ffff7a06028 in QAWindow::qt_metacall(QMetaObject::Call, int, void**)
() from /usr/local/brainvisa-4.3.0/lib/libanatomist.so.4.3.0
#12 0x00007ffff7a059cd in ControlledWindow::qt_metacall(QMetaObject::Call, int, void**) () from /usr/local/brainvisa-4.3.0/lib/libanatomist.so.4.3.0
#13 0x00007ffff7a065d5 in AWindow3D::qt_metacall(QMetaObject::Call, int, void**) () from /usr/local/brainvisa-4.3.0/lib/libanatomist.so.4.3.0
#14 0x00007ffff334cf5c in QMetaObject::activate(QObject*, QMetaObject const*, int, void**) () from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#15 0x00007ffff334a7e5 in QObject::event(QEvent*) ()
from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#16 0x00007ffff54a99ff in QApplicationPrivate::notify_helper(QObject*, QEvent*)
() from /usr/local/brainvisa-4.3.0/lib/libQtGui.so.4
#17 0x00007ffff54acf4b in QApplication::notify(QObject*, QEvent*) ()
from /usr/local/brainvisa-4.3.0/lib/libQtGui.so.4
#18 0x00007ffff333a064 in QCoreApplication::notifyInternal(QObject*, QEvent*)
() from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#19 0x00007ffff33674a0 in ?? ()
from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#20 0x00007ffff3364dc4 in ?? ()
from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#21 0x00007ffff2af4d13 in g_main_context_dispatch ()
from /lib/x86_64-linux-gnu/libglib-2.0.so.0
#22 0x00007ffff2af5060 in ?? () from /lib/x86_64-linux-gnu/libglib-2.0.so.0
---Type <return> to continue, or q <return> to quit---
#23 0x00007ffff2af5124 in g_main_context_iteration ()
from /lib/x86_64-linux-gnu/libglib-2.0.so.0
#24 0x00007ffff336510c in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#25 0x00007ffff5555eff in ?? ()
from /usr/local/brainvisa-4.3.0/lib/libQtGui.so.4
#26 0x00007ffff3339235 in QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#27 0x00007ffff3339556 in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#28 0x00007ffff333b326 in QCoreApplication::exec() ()
from /usr/local/brainvisa-4.3.0/lib/libQtCore.so.4
#29 0x00000000004017b4 in main ()

[riviere]

Hi,
So it really crashes within the OpenGL/DRI implementation. I'm not sure I can help you fix it, but there are still 2 or 3 things you can try:
1. Try the software OpenGL implementation shipped as backup in the brainvisa package (hum, I'm tired, I should have thought about this the first time...). To enable it, move the files in <brainvisa>/lib/mesa to the <brainvisa>/lib/ directory so they are found in the path.
2. try di disable the VTK module of anatomist. I don't think it will change anything, but you can try.
To disable it, move the libanavtk.so.* files out of the lib/ directory of brainvisa (or rename them)
3. try harder to disable hardware or DRI rendering in Xorg. You already tried the option NoAccel I think, you can also try to add in the Modules section of /etc/X11/xorg.conf:

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   Disable "dri"

and restart the X serer (or reboot).
But actually I don't know if it will prevent all 3D to work, or do nothing at all...

If 1 or 3 works, then it will be a low performance solution, but it's still better than nothing...

Denis

[Stephane_Sockeel]

Ok.

The first solution works !

thanks a lot !

I don't try the other sollution...
But I can do it, maybe that will give you some clues.

Stéphane

[riviere]

No no, don't try the other solutions... It will not be better, and now I can live with the idea that it's a bug in your DRI driver and not in Anatomist...