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

[Ida Häggström]

Hi again,
My bad, I read that you WERE using the patch, but you had stated that you
WEREN'T. Disregard the previous email.

Ida

On Mon, Jun 22, 2015 at 2:55 PM, Ida Häggström <ida.haggstrom at umu.se> wrote:

> Hi Pedro!
>
> I know that some people (including myself) have had some problems with
> patch 01 of geant4.10.01 and gate 7.1, at least when compiling. Dunno if
> the problem can be related to the patch or not, but you can try the version
> without the patch: http://geant4.cern.ch/support/source/geant4
> .10.01.tar.gz
>
> Good luck!
> Ida
>
> On Thu, Jun 18, 2015 at 11:19 AM, Pedro Correia <pmcorreia at ua.pt> wrote:
>
>> 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 ()
>> ===========================================================
>>
>>
>>
>>
>
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