[Gate-users] gate crash during Materials.xml loading

[Pedro Correia]

Dear Gaters

I’m having some problems with Gate7.1 and geant4.10.01.

I compile both softwares apparently with no erros, just few warnings in Gate, and when I try to run Gate with some macro file (PET_CylindricalPET_System.mac for example), I got the following output.
I tried to reinstall Root, Geant4 and Gate several times, but I always get the same output. The optical flag is ON.
I think that may be something related with libxml2 library, do you have any suggestion?

Best regards,
Pedro Correia

[Core-0] You are using Geant4 version 10.1.0
[Core-0] Starting macro Optical_System.mac
===== XML PATH ====: ./Materials.xml

 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================

Thread 2 (Thread 0x7eff492f8700 (LWP 9249)):
#0  0x00000039a54df0d3 in poll () from /lib64/libc.so.6
#1  0x00000039a8409aaa in ?? () from /usr/lib64/libxcb.so.1
#2  0x00000039a840b1c8 in xcb_wait_for_event () from /usr/lib64/libxcb.so.1
#3  0x00007eff4b3f23a1 in ?? () from /usr/lib64/qt5/plugins/platforms/libqxcb.so
#4  0x00007eff52fe6819 in ?? () from /usr/lib64/libQt5Core.so.5
#5  0x00000039b40aa754 in ?? () from /usr/lib64/nvidia/libGL.so.1
#6  0x00000039a5c079d1 in start_thread () from /lib64/libpthread.so.0
#7  0x00000039a54e88fd in clone () from /lib64/libc.so.6

Thread 1 (Thread 0x7eff519e4240 (LWP 9248)):
#0  0x00000039a54ac65d in waitpid () from /lib64/libc.so.6
#1  0x00000039a543e609 in do_system () from /lib64/libc.so.6
#2  0x00000039a543e940 in system () from /lib64/libc.so.6
#3  0x0000003867a6a454 in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so
#4  0x0000003867a69873 in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so
#5  <signal handler called>
#6  0x00000039a5529170 in __strncmp_sse42 () from /lib64/libc.so.6
#7  0x00007eff54d5f885 in __xmlParserInputBufferCreateFilename () from /usr/lib64/libxml2.so.2
#8  0x00007eff54d3480d in xmlNewInputFromFile () from /usr/lib64/libxml2.so.2
#9  0x00007eff54d389f6 in xmlCreateURLParserCtxt () from /usr/lib64/libxml2.so.2
#10 0x00007eff54d4d6ae in xmlSAXParseFileWithData () from /usr/lib64/libxml2.so.2
#11 0x00000000008c981a in GateXMLDocument::GateXMLDocument(G4String const&) ()
#12 0x00000000005f0345 in GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&) ()
#13 0x00000000005f24c3 in GateMaterialDatabase::GetMaterial(G4String const&) ()
#14 0x00000000005825cb in GateVVolume::DefineOwnMaterials() ()
#15 0x000000000061edc0 in GateVolumeMessenger::SetNewValue(G4UIcommand*, G4String) ()
#16 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#17 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#18 0x00007eff564c5a97 in G4UIbatch::ExecCommand(G4String const&) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#19 0x00007eff564c6a2b in G4UIbatch::SessionStart() () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#20 0x00007eff564de303 in G4UImanager::ExecuteMacroFile(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#21 0x00007eff564d9648 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#22 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#23 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#24 0x00000000004f83fb 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.
===========================================================
#6  0x00000039a5529170 in __strncmp_sse42 () from /lib64/libc.so.6
#7  0x00007eff54d5f885 in __xmlParserInputBufferCreateFilename () from /usr/lib64/libxml2.so.2
#8  0x00007eff54d3480d in xmlNewInputFromFile () from /usr/lib64/libxml2.so.2
#9  0x00007eff54d389f6 in xmlCreateURLParserCtxt () from /usr/lib64/libxml2.so.2
#10 0x00007eff54d4d6ae in xmlSAXParseFileWithData () from /usr/lib64/libxml2.so.2
#11 0x00000000008c981a in GateXMLDocument::GateXMLDocument(G4String const&) ()
#12 0x00000000005f0345 in GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&) ()
#13 0x00000000005f24c3 in GateMaterialDatabase::GetMaterial(G4String const&) ()
#14 0x00000000005825cb in GateVVolume::DefineOwnMaterials() ()
#15 0x000000000061edc0 in GateVolumeMessenger::SetNewValue(G4UIcommand*, G4String) ()
#16 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#17 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#18 0x00007eff564c5a97 in G4UIbatch::ExecCommand(G4String const&) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#19 0x00007eff564c6a2b in G4UIbatch::SessionStart() () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#20 0x00007eff564de303 in G4UImanager::ExecuteMacroFile(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#21 0x00007eff564d9648 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#22 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#23 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#24 0x00000000004f83fb in main ()
===========================================================