[Gate-users] Error running benchmark for PET

Thu Dec 2 19:47:34 CET 2010

Dear GATE users,

I have recently installed GATE and the first thing I wanted to do was to
run a benchmark.  It seems to run fine (although I question that now),
but when I try running it with visualization by commenting
the /vis/disable line and uncommenting the #control/execute visu.mac
line I get the following:

tuan at ubuntu:~/GATE_ROOT/gate_v6.0_p01/benchmarks/benchPET$ Gate
benchPET.mac
[G4] 
[G4] *************************************************************
[G4]  Geant4 version Name: geant4-09-02-patch-04    (16-September-2010)
[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_v6.0_p01                                           
[Core-0]                     Copyright : OpenGATE
Collaboration                
[Core-0]                     Reference : Phys. Med. Biol. 49 (2004)
4543-4561  
[Core-0]                     WWW :
http://www.opengatecollaboration.org/       
[Core-0]
**********************************************************************
[Core-0] 
[Core-0] Starting macro benchPET.mac

 *** Break *** segmentation violation

===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007fbce9663f7e in waitpid () from /lib/libc.so.6
#1  0x00007fbce95fb7e9 in ?? () from /lib/libc.so.6
#2  0x00007fbcef120821 in TUnixSystem::StackTrace() ()
from /home/tuan/GATE_ROOT/root/lib/libCore.so
#3  0x00007fbcef121913 in TUnixSystem::DispatchSignals(ESignals) ()
from /home/tuan/GATE_ROOT/root/lib/libCore.so
#4  <signal handler called>
#5  0x00007fbcf025f12e in XF86DRIQueryVersion ()
from /usr/lib/fglrx/libGL.so.1
#6  0x00007fbcf025f2c9 in XF86DRIQueryExtension ()
from /usr/lib/fglrx/libGL.so.1
#7  0x00007fbcf025ec70 in ?? () from /usr/lib/fglrx/libGL.so.1
#8  0x00007fbcf023eff8 in ?? () from /usr/lib/fglrx/libGL.so.1
#9  0x00007fbcf0239146 in glXChooseVisual ()
from /usr/lib/fglrx/libGL.so.1
#10 0x00000000006a774f in
G4OpenGLXViewer::G4OpenGLXViewer(G4OpenGLSceneHandler&) ()
#11 0x000000000069bd85 in
G4OpenGLStoredXViewer::G4OpenGLStoredXViewer(G4OpenGLStoredSceneHandler&, G4String const&) ()
#12 0x000000000069b214 in
G4OpenGLStoredX::CreateViewer(G4VSceneHandler&, G4String const&) ()
#13 0x00000000006e178d in G4VisManager::CreateViewer(G4String, G4String)
()
#14 0x000000000071a68b in
G4VisCommandViewerCreate::SetNewValue(G4UIcommand*, G4String) ()
#15 0x0000000000f7b20e in G4UIcommand::DoIt(G4String) ()
#16 0x0000000000f83154 in G4UImanager::ApplyCommand(char const*) ()
#17 0x00000000006f0742 in G4VisCommandOpen::SetNewValue(G4UIcommand*,
G4String) ()
#18 0x0000000000f7b20e in G4UIcommand::DoIt(G4String) ()
#19 0x0000000000f83154 in G4UImanager::ApplyCommand(char const*) ()
#20 0x0000000000f8e1e9 in G4UIbatch::ExecCommand(G4String const&) ()
#21 0x0000000000f8f0b9 in G4UIbatch::SessionStart() ()
#22 0x0000000000f810c3 in G4UImanager::ExecuteMacroFile(char const*) ()
#23 0x0000000000f8f494 in
G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) ()
#24 0x0000000000f7b20e in G4UIcommand::DoIt(G4String) ()
#25 0x0000000000f83154 in G4UImanager::ApplyCommand(char const*) ()
#26 0x0000000000f8e1e9 in G4UIbatch::ExecCommand(G4String const&) ()
#27 0x0000000000f8f0b9 in G4UIbatch::SessionStart() ()
#28 0x0000000000f810c3 in G4UImanager::ExecuteMacroFile(char const*) ()
#29 0x0000000000f8f494 in
G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) ()
#30 0x0000000000f7b20e in G4UIcommand::DoIt(G4String) ()
#31 0x0000000000f83154 in G4UImanager::ApplyCommand(char const*) ()
#32 0x0000000000645612 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.
===========================================================
#5  0x00007fbcf025f12e in XF86DRIQueryVersion ()
from /usr/lib/fglrx/libGL.so.1
#6  0x00007fbcf025f2c9 in XF86DRIQueryExtension ()
from /usr/lib/fglrx/libGL.so.1
#7  0x00007fbcf025ec70 in ?? () from /usr/lib/fglrx/libGL.so.1
#8  0x00007fbcf023eff8 in ?? () from /usr/lib/fglrx/libGL.so.1
#9  0x00007fbcf0239146 in glXChooseVisual ()
from /usr/lib/fglrx/libGL.so.1
#10 0x00000000006a774f in
G4OpenGLXViewer::G4OpenGLXViewer(G4OpenGLSceneHandler&) ()
#11 0x000000000069bd85 in
G4OpenGLStoredXViewer::G4OpenGLStoredXViewer(G4OpenGLStoredSceneHandler&, G4String const&) ()
#12 0x000000000069b214 in
G4OpenGLStoredX::CreateViewer(G4VSceneHandler&, G4String const&) ()
#13 0x00000000006e178d in G4VisManager::CreateViewer(G4String, G4String)
()
#14 0x000000000071a68b in
G4VisCommandViewerCreate::SetNewValue(G4UIcommand*, G4String) ()
#15 0x0000000000f7b20e in G4UIcommand::DoIt(G4String) ()
#16 0x0000000000f83154 in G4UImanager::ApplyCommand(char const*) ()
#17 0x00000000006f0742 in G4VisCommandOpen::SetNewValue(G4UIcommand*,
G4String) ()
#18 0x0000000000f7b20e in G4UIcommand::DoIt(G4String) ()
#19 0x0000000000f83154 in G4UImanager::ApplyCommand(char const*) ()
#20 0x0000000000f8e1e9 in G4UIbatch::ExecCommand(G4String const&) ()
#21 0x0000000000f8f0b9 in G4UIbatch::SessionStart() ()
#22 0x0000000000f810c3 in G4UImanager::ExecuteMacroFile(char const*) ()
#23 0x0000000000f8f494 in
G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) ()
#24 0x0000000000f7b20e in G4UIcommand::DoIt(G4String) ()
#25 0x0000000000f83154 in G4UImanager::ApplyCommand(char const*) ()
#26 0x0000000000f8e1e9 in G4UIbatch::ExecCommand(G4String const&) ()
#27 0x0000000000f8f0b9 in G4UIbatch::SessionStart() ()
#28 0x0000000000f810c3 in G4UImanager::ExecuteMacroFile(char const*) ()
#29 0x0000000000f8f494 in
G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) ()
#30 0x0000000000f7b20e in G4UIcommand::DoIt(G4String) ()
#31 0x0000000000f83154 in G4UImanager::ApplyCommand(char const*) ()
#32 0x0000000000645612 in main ()
===========================================================

Now I am fairly new to linux (I just began learning it in order to use
GATE) so the error message seems pretty foreign to me.  Does anyone know
why GATE is crashing?

Also whenever I start GATE, I notice that it gives me a prompt with
Idle> instead of Preinit> like the tutorials say it does.  Is that a
problem?

Thanks,
Tuan Huynh