[Gate-users] Error running benchmark for PET with visualisation on Ubuntu
Paweł Kowalski
flukson at gmail.com
Mon Oct 15 13:08:58 CEST 2012
Hello,
When I run benchmark for PET with enabled visualisation on Ubuntu, I get
the error listed below. Is this problem caused by the lack of any library?
I would be grateful for any help. I don't have this error when
visualisation is disabled.
Best regards,
Paweł Kowalski
[G4]
[G4] *************************************************************
[G4] Geant4 version Name: geant4-09-05-patch-01 (20-March-2012)
[G4] Copyright : Geant4 Collaboration
[G4] Reference : NIM A 506 (2003), 250-303
[G4] WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4]
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Core-0] Initialization of actors
[Core-0]
[Core-0]
**********************************************************************
[Core-0] GATE version name: gate_v6.2
[Core-0] Copyright : OpenGATE Collaboration
[Core-0] Reference : Phys. Med. Biol. 49 (2004)
4543-4561
[Core-0] Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0] WWW : http://www.opengatecollaboration.org
[Core-0]
**********************************************************************
[Core-0]
[Core-0] Starting macro benchPET.mac
*** Break *** segmentation violation
===========================================================
There was a crash (#8 0xb532860b in SigHandler(ESignals) () from
/opt/root/lib/libCore.so).
This is the entire stack trace of all threads:
===========================================================
Thread 5 (Thread 0xaf92db40 (LWP 11506)):
#0 0xb77ae424 in __kernel_vsyscall ()
#1 0xb427d800 in poll () from /lib/libc.so.6
#2 0xb2411d0b in g_poll () from /lib/i386-linux-gnu/libglib-2.0.so.0
#3 0xb240406e in ?? () from /lib/i386-linux-gnu/libglib-2.0.so.0
#4 0xb240452b in g_main_loop_run () from
/lib/i386-linux-gnu/libglib-2.0.so.0
#5 0xb09b4134 in ?? () from
/usr/lib/i386-linux-gnu/gio/modules/libdconfsettings.so
#6 0xb24288f3 in ?? () from /lib/i386-linux-gnu/libglib-2.0.so.0
#7 0xb434dd4c in start_thread () from /lib/i386-linux-gnu/libpthread.so.0
#8 0xb428bf4e in clone () from /lib/libc.so.6
Thread 4 (Thread 0xaefffb40 (LWP 11507)):
#0 0xb77ae424 in __kernel_vsyscall ()
#1 0xb427d800 in poll () from /lib/libc.so.6
#2 0xb2411d0b in g_poll () from /lib/i386-linux-gnu/libglib-2.0.so.0
#3 0xb240406e in ?? () from /lib/i386-linux-gnu/libglib-2.0.so.0
#4 0xb240452b in g_main_loop_run () from
/lib/i386-linux-gnu/libglib-2.0.so.0
#5 0xb086ac1a in ?? () from /usr/lib/i386-linux-gnu/libgio-2.0.so.0
#6 0xb24288f3 in ?? () from /lib/i386-linux-gnu/libglib-2.0.so.0
#7 0xb434dd4c in start_thread () from /lib/i386-linux-gnu/libpthread.so.0
#8 0xb428bf4e in clone () from /lib/libc.so.6
Thread 3 (Thread 0xae5ffb40 (LWP 11508)):
#0 0xb77ae424 in __kernel_vsyscall ()
#1 0xb4351d13 in pthread_cond_timedwait
GLIBC_2.3.2 () from /lib/i386-linux-gnu/libpthread.so.0
#2 0xb2444bf0 in g_cond_wait_until () from
/lib/i386-linux-gnu/libglib-2.0.so.0
#3 0xb23d74e9 in ?? () from /lib/i386-linux-gnu/libglib-2.0.so.0
#4 0xb23d7d0e in g_async_queue_timeout_pop () from
/lib/i386-linux-gnu/libglib-2.0.so.0
#5 0xb24291cc in ?? () from /lib/i386-linux-gnu/libglib-2.0.so.0
#6 0xb24288f3 in ?? () from /lib/i386-linux-gnu/libglib-2.0.so.0
#7 0xb434dd4c in start_thread () from /lib/i386-linux-gnu/libpthread.so.0
#8 0xb428bf4e in clone () from /lib/libc.so.6
Thread 2 (Thread 0xadbffb40 (LWP 11509)):
#0 0xb77ae424 in __kernel_vsyscall ()
#1 0xb4284f71 in select () from /lib/libc.so.6
#2 0xb31f8e26 in ?? () from /usr/lib/i386-linux-gnu/libQtCore.so.4
#3 0xb3109de0 in ?? () from /usr/lib/i386-linux-gnu/libQtCore.so.4
#4 0xb434dd4c in start_thread () from /lib/i386-linux-gnu/libpthread.so.0
#5 0xb428bf4e in clone () from /lib/libc.so.6
Thread 1 (Thread 0xb22e9740 (LWP 11505)):
#0 0xb77ae424 in __kernel_vsyscall ()
#1 0xb4254b7b in waitpid () from /lib/libc.so.6
#2 0xb41dc003 in ?? () from /lib/libc.so.6
#3 0xb41dc4ba in system () from /lib/libc.so.6
#4 0xb4355e2b in system () from /lib/i386-linux-gnu/libpthread.so.0
#5 0xb532140b in TUnixSystem::Exec(char const*) () from
/opt/root/lib/libCore.so
#6 0xb53259d0 in TUnixSystem::StackTrace() () from /opt/root/lib/libCore.so
#7 0xb53284f7 in TUnixSystem::DispatchSignals(ESignals) () from
/opt/root/lib/libCore.so
#8 0xb532860b in SigHandler(ESignals) () from /opt/root/lib/libCore.so
#9 0xb531f642 in sighandler(int) () from /opt/root/lib/libCore.so
#10 <signal handler called>
#11 0xb3231d0a in QObject::blockSignals(bool) () from
/usr/lib/i386-linux-gnu/libQtCore.so.4
#12 0xb7681eb4 in G4OpenGLQtViewer::addTreeElement(G4String,
std::vector<std::pair<std::string, std::pair<unsigned int, unsigned int> >,
std::allocator<std::pair<std::string, std::pair<unsigned int, unsigned int>
> > >) () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#13 0xb76835cf in G4OpenGLStoredQtSceneHandler::ExtraPOProcessing(unsigned
int) () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#14 0xb765bb50 in
G4OpenGLStoredSceneHandler::AddPrimitivePreamble(G4Visible const&) [clone
.part.189] () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#15 0xb765be91 in G4OpenGLStoredSceneHandler::AddPrimitive(G4Polyhedron
const&) () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#16 0xb75b2dc7 in G4VSceneHandler::RequestPrimitives(G4VSolid const&) ()
from /opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#17 0xb765c1bb in G4OpenGLStoredSceneHandler::RequestPrimitives(G4VSolid
const&) () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#18 0xb75b154a in G4VSceneHandler::AddSolid(G4Box const&) () from
/opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#19 0xb76544b3 in G4OpenGLSceneHandler::AddSolid(G4Box const&) () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#20 0xb5b4c477 in G4Box::DescribeYourselfTo(G4VGraphicsScene&) const ()
from /opt/geant4.9.5.p01-install/lib/libG4geometry.so
#21 0xb75357c3 in G4PhysicalVolumeModel::DescribeSolid(HepGeom::Transform3D
const&, G4VSolid*, G4VisAttributes const*, G4VGraphicsScene&) () from
/opt/geant4.9.5.p01-install/lib/libG4modeling.so
#22 0xb7536aa6 in
G4PhysicalVolumeModel::DescribeAndDescend(G4VPhysicalVolume*, int,
G4LogicalVolume*, G4VSolid*, G4Material*, HepGeom::Transform3D const&,
G4VGraphicsScene&) () from /opt/geant4.9.5.p01-install/lib/libG4modeling.so
#23 0xb753722a in
G4PhysicalVolumeModel::VisitGeometryAndGetVisReps(G4VPhysicalVolume*, int,
HepGeom::Transform3D const&, G4VGraphicsScene&) () from
/opt/geant4.9.5.p01-install/lib/libG4modeling.so
#24 0xb75382de in
G4PhysicalVolumeModel::DescribeYourselfTo(G4VGraphicsScene&) () from
/opt/geant4.9.5.p01-install/lib/libG4modeling.so
#25 0xb75b276b in G4VSceneHandler::ProcessScene(G4VViewer&) () from
/opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#26 0xb75b61a2 in G4VViewer::ProcessView() () from
/opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#27 0xb768490d in G4OpenGLStoredQtViewer::ComputeView() () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#28 0xb7684ac4 in G4OpenGLStoredQtViewer::paintGL() () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#29 0xb3e76c43 in QGLWidget::glDraw() () from
/usr/lib/i386-linux-gnu/libQtOpenGL.so.4
#30 0xb3e764bb in QGLWidget::updateGL() () from
/usr/lib/i386-linux-gnu/libQtOpenGL.so.4
#31 0xb7683d81 in G4OpenGLStoredQtViewer::updateQWidget() () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#32 0xb7683d2f in G4OpenGLStoredQtViewer::DrawView() () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#33 0xb75e8316 in G4VisCommandSceneHandlerAttach::SetNewValue(G4UIcommand*,
G4String) () from /opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#34 0xb590e918 in G4UIcommand::DoIt(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#35 0xb5924e4e in G4UImanager::ApplyCommand(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#36 0xb75bfb14 in G4VisCommandDrawVolume::SetNewValue(G4UIcommand*,
G4String) () from /opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#37 0xb590e918 in G4UIcommand::DoIt(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#38 0xb5924e4e in G4UImanager::ApplyCommand(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#39 0xb5925525 in G4UImanager::ApplyCommand(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#40 0xb58fefd5 in G4UIbatch::ExecCommand(G4String const&) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#41 0xb59002f7 in G4UIbatch::SessionStart() () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#42 0xb592093e in G4UImanager::ExecuteMacroFile(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#43 0xb5919b19 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String)
() from /opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#44 0xb590e918 in G4UIcommand::DoIt(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#45 0xb5924e4e in G4UImanager::ApplyCommand(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#46 0xb5925525 in G4UImanager::ApplyCommand(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#47 0xb58fefd5 in G4UIbatch::ExecCommand(G4String const&) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#48 0xb59002f7 in G4UIbatch::SessionStart() () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#49 0xb592093e in G4UImanager::ExecuteMacroFile(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#50 0xb5919b19 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String)
() from /opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#51 0xb590e918 in G4UIcommand::DoIt(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#52 0xb5924e4e in G4UImanager::ApplyCommand(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#53 0xb5925525 in G4UImanager::ApplyCommand(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#54 0x080fe95a in main ()
===========================================================
The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#11 0xb3231d0a in QObject::blockSignals(bool) () from
/usr/lib/i386-linux-gnu/libQtCore.so.4
#12 0xb7681eb4 in G4OpenGLQtViewer::addTreeElement(G4String,
std::vector<std::pair<std::string, std::pair<unsigned int, unsigned int> >,
std::allocator<std::pair<std::string, std::pair<unsigned int, unsigned int>
> > >) () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#13 0xb76835cf in G4OpenGLStoredQtSceneHandler::ExtraPOProcessing(unsigned
int) () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#14 0xb765bb50 in
G4OpenGLStoredSceneHandler::AddPrimitivePreamble(G4Visible const&) [clone
.part.189] () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#15 0xb765be91 in G4OpenGLStoredSceneHandler::AddPrimitive(G4Polyhedron
const&) () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#16 0xb75b2dc7 in G4VSceneHandler::RequestPrimitives(G4VSolid const&) ()
from /opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#17 0xb765c1bb in G4OpenGLStoredSceneHandler::RequestPrimitives(G4VSolid
const&) () from /opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#18 0xb75b154a in G4VSceneHandler::AddSolid(G4Box const&) () from
/opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#19 0xb76544b3 in G4OpenGLSceneHandler::AddSolid(G4Box const&) () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#20 0xb5b4c477 in G4Box::DescribeYourselfTo(G4VGraphicsScene&) const ()
from /opt/geant4.9.5.p01-install/lib/libG4geometry.so
#21 0xb75357c3 in G4PhysicalVolumeModel::DescribeSolid(HepGeom::Transform3D
const&, G4VSolid*, G4VisAttributes const*, G4VGraphicsScene&) () from
/opt/geant4.9.5.p01-install/lib/libG4modeling.so
#22 0xb7536aa6 in
G4PhysicalVolumeModel::DescribeAndDescend(G4VPhysicalVolume*, int,
G4LogicalVolume*, G4VSolid*, G4Material*, HepGeom::Transform3D const&,
G4VGraphicsScene&) () from /opt/geant4.9.5.p01-install/lib/libG4modeling.so
#23 0xb753722a in
G4PhysicalVolumeModel::VisitGeometryAndGetVisReps(G4VPhysicalVolume*, int,
HepGeom::Transform3D const&, G4VGraphicsScene&) () from
/opt/geant4.9.5.p01-install/lib/libG4modeling.so
#24 0xb75382de in
G4PhysicalVolumeModel::DescribeYourselfTo(G4VGraphicsScene&) () from
/opt/geant4.9.5.p01-install/lib/libG4modeling.so
#25 0xb75b276b in G4VSceneHandler::ProcessScene(G4VViewer&) () from
/opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#26 0xb75b61a2 in G4VViewer::ProcessView() () from
/opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#27 0xb768490d in G4OpenGLStoredQtViewer::ComputeView() () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#28 0xb7684ac4 in G4OpenGLStoredQtViewer::paintGL() () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#29 0xb3e76c43 in QGLWidget::glDraw() () from
/usr/lib/i386-linux-gnu/libQtOpenGL.so.4
#30 0xb3e764bb in QGLWidget::updateGL() () from
/usr/lib/i386-linux-gnu/libQtOpenGL.so.4
#31 0xb7683d81 in G4OpenGLStoredQtViewer::updateQWidget() () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#32 0xb7683d2f in G4OpenGLStoredQtViewer::DrawView() () from
/opt/geant4.9.5.p01-install/lib/libG4OpenGL.so
#33 0xb75e8316 in G4VisCommandSceneHandlerAttach::SetNewValue(G4UIcommand*,
G4String) () from /opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#34 0xb590e918 in G4UIcommand::DoIt(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#35 0xb5924e4e in G4UImanager::ApplyCommand(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#36 0xb75bfb14 in G4VisCommandDrawVolume::SetNewValue(G4UIcommand*,
G4String) () from /opt/geant4.9.5.p01-install/lib/libG4vis_management.so
#37 0xb590e918 in G4UIcommand::DoIt(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#38 0xb5924e4e in G4UImanager::ApplyCommand(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#39 0xb5925525 in G4UImanager::ApplyCommand(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#40 0xb58fefd5 in G4UIbatch::ExecCommand(G4String const&) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#41 0xb59002f7 in G4UIbatch::SessionStart() () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#42 0xb592093e in G4UImanager::ExecuteMacroFile(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#43 0xb5919b19 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String)
() from /opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#44 0xb590e918 in G4UIcommand::DoIt(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#45 0xb5924e4e in G4UImanager::ApplyCommand(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#46 0xb5925525 in G4UImanager::ApplyCommand(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#47 0xb58fefd5 in G4UIbatch::ExecCommand(G4String const&) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#48 0xb59002f7 in G4UIbatch::SessionStart() () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#49 0xb592093e in G4UImanager::ExecuteMacroFile(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#50 0xb5919b19 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String)
() from /opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#51 0xb590e918 in G4UIcommand::DoIt(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#52 0xb5924e4e in G4UImanager::ApplyCommand(char const*) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#53 0xb5925525 in G4UImanager::ApplyCommand(G4String) () from
/opt/geant4.9.5.p01-install/lib/libG4intercoms.so
#54 0x080fe95a in main ()
===========================================================
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