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

[Pedro Correia]

Dear Gaters

Since I was not the only one having this problem (the user Gwennaëlle MARIN had the same experience few weeks ago).
We both used Scientific Linux 6, gate v7.1 and geant4.10.01 (no patch-01).

I’m assuming that is not an issue with Geant4, because I found nothing related with this in the Geant4 forum.
Is it possible that the Gate developers take a look to this?

Cheers, Pedro




No dia 16/06/2015, às 18:50, pedro correia <pmcorreia at ua.pt<mailto:pmcorreia at ua.pt>> escreveu:

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 ()
===========================================================



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20150618/13de420a/attachment-0001.html>