[Gate-users] core dumps

[Mojca Miklavec]

Hello,

I tried to compile Gate from master branch of the git repository. I
have Geant4 9.5.p02 and CLHEP 2.1.3.1 installed and I'm testing this
on Mac OS X 10.7.

I first had to apply the following patches (otherwise Gate wouldn't
compile at all):

--- source/general/include/GateUIcmdWithAVector.hh
+++ source/general/include/GateUIcmdWithAVector.hh
@@ -118,14 +118,14 @@ template<typename vContentType>
 G4String GateUIcmdWithAVector<vContentType>::ConvertToString
 (std::vector<vContentType> vec)
 {
-  char st[100];
+  //char st[100];
   //LF
   //std::ostrstream os(st,100);
-  std::ostringstream os(st,100);
+  std::ostringstream os;
   //LF
   for (G4int i=0; i<vec.size(); i++) os << vec[i] << " ";
   os << '\0';
-  G4String vl = st;
+  G4String vl = os.str();
   G4cout << "GateUIcmdWithAVector::ConvertToString : " << vl << G4endl;
   return vl;
 }
--- source/physics/src/GateBinaryCascade.cc
+++ source/physics/src/GateBinaryCascade.cc
@@ -2278,7 +2278,7 @@ G4Fragment * GateBinaryCascade::FindFragments()
   }

   G4int zCaptured = 0;
-  G4LorentzVector CapturedMomentum=0;
+  G4LorentzVector CapturedMomentum(0);
   for(i = theCapturedList.begin(); i != theCapturedList.end(); ++i)
   {
       CapturedMomentum += (*i)->Get4Momentum();
@@ -2392,7 +2392,7 @@ G4LorentzVector
GateBinaryCascade::GetFinalNucleusMomentum()
 // return momentum of nucleus for use with precompound model; also
keep transformation to
 //   apply to precompoud products.

-  G4LorentzVector CapturedMomentum=0;
+  G4LorentzVector CapturedMomentum(0);
   G4KineticTrackVector::iterator i;
 //  G4cout << "GetFinalNucleusMomentum Captured size: "
<<theCapturedList.size() << G4endl;
   for(i = theCapturedList.begin(); i != theCapturedList.end(); ++i)


It compiled and installed successfully, but when I try to run any
examples, it usually crashes. Here's what's reported from

example_CT/fast> Gate --qt benchmarkFastCT.mac


-------- EEEE ------- G4Exception-START -------- EEEE -------

*** G4Exception : DecodingException

issued by : GateMDBFieldDecoder::DecodingException

The definition of the element/material 'Air' is incorrect: The unit
found for the density field ('.29 mg/cm3')

is not in the list of autorised units
('g/cm3','g/m3','g/mm3','kg/cm3','kg/m3','kg/mm3','mg/cm3','mg/m3','mg/mm3')
for this field.

You should check this definition in the database file.

*** Fatal Exception *** core dump ***

-------- EEEE -------- G4Exception-END --------- EEEE -------


And here's where it crashes with

example_CT/fast> Gate benchmarkFastCT.mac


> Gate benchmarkFastCT.mac
[G4]
[G4] *************************************************************
[G4]  Geant4 version Name: geant4-09-05-patch-02    (22-October-2012)
[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_v6.2
[Core-0]                     Copyright : OpenGATE Collaboration
[Core-0]                     Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0]                     Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0]                     WWW : http://www.opengatecollaboration.org
[Core-0] **********************************************************************
[Core-0]
[Core-0] You are using a 9.5 version of Geant4
[Core-0] Starting macro benchmarkFastCT.mac
 Rmin/gate/aluminiumBall/geometry/setRmin
 Rmin/gate/PVCBall/geometry/setRmin
 Rmin/gate/glassBall/geometry/setRmin
 Rmin/gate/spineBoneBall/geometry/setRmin
 <!> *** WARNING *** <!>  Unknown process: MultipleScattering


List of Enabled processes:


   ===  Process: Bremsstrahlung  ===
Particle: e+
    * Model(s):
       - <!> *** Warning *** <!> No model selected!
Particle: e-
    * Model(s):
       - StandardModel

   ===  Process: Compton  ===
Particle: gamma
    * Model(s):
       - PenelopeModel

   ===  Process: ElectronIonisation  ===
Particle: e+
    * Model(s):
       - <!> *** Warning *** <!> No model selected!
Particle: e-
    * Model(s):
       - StandardModel

   ===  Process: PhotoElectric  ===
Particle: gamma
    * Model(s):
       - StandardModel

   ===  Process: RayleighScattering  ===
Particle: gamma
    * Model(s):
       - PenelopeModel




List of initialized processes:



Verbosity Set to: 0
GateSourceMgr::ListSources: List of the sources in the source manager
Source --------------> xraygun
  ID                 : 0
  type               : gps
  activity (Bq)      : 350000
  startTime (s)      : 0
  time (s)           : 0
  forcedUnstable     : 0
  forcedHalfLife (s) : -0.693147
  verboseLevel       : 0
  relative to vol    : World
----------------------

[Core-0] Initialization of geometry
[Core-0] Initialization of physics

-------- EEEE ------- G4Exception-START -------- EEEE -------
*** G4Exception : em0006
      issued by : G4AugerData::LoadData

*** Fatal Exception *** core dump ***
-------- EEEE -------- G4Exception-END --------- EEEE -------


*** G4Exception: Aborting execution ***
Abort trap: 6

Any hints would be appreciated.

Mojca