[Gate-users] Surfaces.xml and Materials.xml problem

[Beien Wang]

Dear GATE users,

I just installed Gate 7.1 on a CentOS6.6 cluster. The installation went
smoothly and Gate works well with gamma photon simulations. But when I turn
to optical simulations, the simulation crashes whenever I refer to any
surfaces in Surfaces.xml and a few materials in Materials.xml, e.g. Water.

I set OPTICAL flag ON when compiling Gate. One possibility I can think of
is that I did not set OpenGL or X11 flag ON when I install GEANT4, since I
am not interested in visualizing the process in the cluster. But when
compiling ROOT, I kept the default X11 and OpenGL flags ON. Could it be the
reason? Thank you!

Best,
Beien

The error message is attached:

===== XML PATH ====: ./Materials.xml

 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007f7965a7d61e in waitpid () from /lib64/libc.so.6
#1  0x00007f7965a0f609 in do_system () from /lib64/libc.so.6
#2  0x00007f796ace8848 in TUnixSystem::StackTrace (this=0x1ee0090) at
/home/beienwang/root/core/unix/src/TUnixSystem.cxx:2419
#3  0x00007f796ace76c3 in TUnixSystem::DispatchSignals (this=0x1ee0090,
sig=kSigSegmentationViolation) at
/home/beienwang/root/core/unix/src/TUnixSystem.cxx:1294
#4  <signal handler called>
#5  0x00007f7965afa2f0 in __strncmp_sse42 () from /lib64/libc.so.6
#6  0x00007f79669a8885 in __xmlParserInputBufferCreateFilename () from
/usr/lib64/libxml2.so.2
#7  0x00007f796697d80d in xmlNewInputFromFile () from
/usr/lib64/libxml2.so.2
#8  0x00007f79669819f6 in xmlCreateURLParserCtxt () from
/usr/lib64/libxml2.so.2
#9  0x00007f79669966ae in xmlSAXParseFileWithData () from
/usr/lib64/libxml2.so.2
#10 0x00000000008679a0 in GateXMLDocument::GateXMLDocument(G4String const&)
()
#11 0x0000000000579c19 in
GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&) ()
#12 0x000000000057bc3b in GateMaterialDatabase::GetMaterial(G4String
const&) ()
#13 0x000000000057f7f8 in GateVVolume::DefineOwnMaterials() ()
#14 0x00000000005bd630 in GateVolumeMessenger::SetNewValue(G4UIcommand*,
G4String) ()
#15 0x00007f796bafc2cb in G4UIcommand::DoIt(G4String) () from
/home/beienwang/programme/geant4/geant4.10.01-install/lib64/libG4intercoms.so
#16 0x00007f796bb096b7 in G4UImanager::ApplyCommand(char const*) () from
/home/beienwang/programme/geant4/geant4.10.01-install/lib64/libG4intercoms.so
#17 0x00007f796fd5687c in G4UIterminal::ExecuteCommand(G4String const&) ()
from
/home/beienwang/programme/geant4/geant4.10.01-install/lib64/libG4interfaces.so
#18 0x00007f796fd57ec4 in G4UIterminal::SessionStart() () from
/home/beienwang/programme/geant4/geant4.10.01-install/lib64/libG4interfaces.so
#19 0x00000000004f1b8e 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  0x00007f7965afa2f0 in __strncmp_sse42 () from /lib64/libc.so.6
#6  0x00007f79669a8885 in __xmlParserInputBufferCreateFilename () from
/usr/lib64/libxml2.so.2
#7  0x00007f796697d80d in xmlNewInputFromFile () from
/usr/lib64/libxml2.so.2
#8  0x00007f79669819f6 in xmlCreateURLParserCtxt () from
/usr/lib64/libxml2.so.2
#9  0x00007f79669966ae in xmlSAXParseFileWithData () from
/usr/lib64/libxml2.so.2
#10 0x00000000008679a0 in GateXMLDocument::GateXMLDocument(G4String const&)
()
#11 0x0000000000579c19 in
GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&) ()
#12 0x000000000057bc3b in GateMaterialDatabase::GetMaterial(G4String
const&) ()
#13 0x000000000057f7f8 in GateVVolume::DefineOwnMaterials() ()
#14 0x00000000005bd630 in GateVolumeMessenger::SetNewValue(G4UIcommand*,
G4String) ()
#15 0x00007f796bafc2cb in G4UIcommand::DoIt(G4String) () from
/home/beienwang/programme/geant4/geant4.10.01-install/lib64/libG4intercoms.so
#16 0x00007f796bb096b7 in G4UImanager::ApplyCommand(char const*) () from
/home/beienwang/programme/geant4/geant4.10.01-install/lib64/libG4intercoms.so
#17 0x00007f796fd5687c in G4UIterminal::ExecuteCommand(G4String const&) ()
from
/home/beienwang/programme/geant4/geant4.10.01-install/lib64/libG4interfaces.so
#18 0x00007f796fd57ec4 in G4UIterminal::SessionStart() () from
/home/beienwang/programme/geant4/geant4.10.01-install/lib64/libG4interfaces.so
#19 0x00000000004f1b8e in main ()
===========================================================


Segmentation fault (core dumped)
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