[Gate-users] CT example

Fatimah Alyami fatimaalfahhad8 at gmail.com
Mon Apr 1 00:25:05 CEST 2019 

Dear all,

I tried to run the CT example provided in this link:
http://www.opengatecollaboration.org/Materials2015/PracticalExercises2015/CT

The name of file of example is: tp_CT.tar.gz

I followed the instruction in the "questions.txt" file but I didn't get the
expected output; instead it said that there was a crash.

This is the full output I got after running the "simu_ct.mac" file:

[G4]
[G4] **************************************************************
[G4]  Geant4 version Name: geant4-10-04-patch-02    (25-May-2018)
[G4]                        Copyright : Geant4 Collaboration
[G4]                       References : NIM A 506 (2003), 250-303
[G4]                                  : IEEE-TNS 53 (2006), 270-278
[G4]                                  : NIM A 835 (2016), 186-225
[G4]                              WWW : http://geant4.org/
[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 8.1.p01 (April 2018)
[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]  Reference : Med. Phys. 41(6)    (2014)
[Core-0]  http://www.opengatecollaboration.org
[Core-0] *************************************************
[Core-0]
[Core-0] You are using Geant4 version 10.4.2
[Core-0] Starting macro simu_ct.mac
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--10-100-75-75-m-60-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--11-80-100-100-m-60-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--12-120-75-75-m-70-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--14-100-100-100-m-90-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--17-120-100-100-m-100-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--18-180-75-75-m-110-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--20-140-100-100-m-110-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--24-240-75-75-m-150-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--25-180-100-100-m-150-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--34-240-100-100-m-200-iso8859-1
/tracking/storeTrajectory 1
Attributes available for modeling and filtering with
  "/vis/modeling/trajectories/create/drawByAttribute" and
  "/vis/filtering/trajectories/create/attributeFilter" commands:
G4TrajectoriesModel:
  Event ID (EventID): G4int
  Run ID (RunID): G4int
G4Trajectory:
  Charge (Ch): unit: e+ (G4double)
  Track ID (ID): G4int
  Initial kinetic energy (IKE): G4BestUnit (G4double)
  Initial momentum magnitude (IMag): G4BestUnit (G4double)
  Initial momentum (IMom): G4BestUnit (G4ThreeVector)
  No. of points (NTP): G4int
  PDG Encoding (PDG): G4int
  Parent ID (PID): G4int
  Particle Name (PN): G4String
G4TrajectoryPoint:
  Position (Pos): G4BestUnit (G4ThreeVector)
WARNING: Trajectory storing has been requested.  This action may be
  reversed with "/tracking/storeTrajectory 0".
0: RINDEX
1.84e-06   1.00028
4.08e-06   1.00028
9: GROUPVEL
1.84e-06   299.709
4.08e-06   299.709
14: ABSLENGTH
1.84e-06   50000
4.08e-06   50000
0: RINDEX
1e-06   1.33
5e-06   1.33
6e-06   1.33
7e-06   1.33
9: GROUPVEL
1e-06   225.408
3e-06   225.408
5.5e-06   225.408
7e-06   225.408
10: MIEHG
1e-06   2.3
5e-06   1.3
6e-06   3.2
7e-06   6.7
5: MIEHG_FORWARD
0.6
6: MIEHG_BACKWARD
0.6
7: MIEHG_FORWARD_RATIO
1
 Rmin/gate/aluminiumBall/geometry/setRmin
 Rmin/gate/spineBoneBall/geometry/setRmin


List of Enabled processes:


   ===  Process: Bremsstrahlung  ===
Particle: e+
    * Model(s):
       - StandardModel
Particle: e-
    * Model(s):
       - StandardModel

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

   ===  Process: ElectronIonisation  ===
Particle: e+
    * Model(s):
       - StandardModel
Particle: e-
    * Model(s):
       - StandardModel

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

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

   ===  Process: eMultipleScattering  ===
Particle: e+
    * Model(s):
       - UrbanModel
Particle: e-
    * Model(s):
       - UrbanModel



List of initialized processes:


[Core-0] Initialization of geometry
G4PhysicalVolumeModel::Validate(): A volume of the same name and
  copy number ("world_phys", copy 0) still exists and is being used.
  But it is not the same volume you originally specified
  in /vis/scene/add/.
[Core-0] Initialization of physics
[Physic-0] WARNING: manual physic lists are being deprecated.
Please, use physic list builder mechanism instead. Related documentation
can be found at:
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics
[Core-0] Initialization of actors
GateSourceMgr::ListSources: List of the sources in the source manager
Source --------------> xraygun
  ID                 : 0
  type               : gps
  activity (Bq)      : 0
  startTime (s)      : 0
  time (s)           : 0
  forcedUnstable     : 0
  forcedHalfLife (s) : -0.693147
  verboseLevel       : 0
  relative to vol    : world
----------------------

[Core-0] End of macro simu_ct.mac
GateOutputMgr deleting...
Graphics systems deleted.
Visualization Manager deleting...

 *** Break *** segmentation violation



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

Thread 3 (Thread 0x7fc415ea6700 (LWP 20470)):
#0  0x00007fc435fdf9f3 in futex_wait_cancelable (private=<optimized out>,
expected=0, futex_word=0x5602f3c3198c) at
../sysdeps/unix/sysv/linux/futex-internal.h:88
#1  0x00007fc435fdf9f3 in __pthread_cond_wait_common (abstime=0x0,
mutex=0x5602f3c31938, cond=0x5602f3c31960) at pthread_cond_wait.c:502
#2  0x00007fc435fdf9f3 in __pthread_cond_wait (cond=0x5602f3c31960,
mutex=0x5602f3c31938) at pthread_cond_wait.c:655
#3  0x00007fc41b78bd5b in  () at /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
#4  0x00007fc41b78bbd7 in  () at /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
#5  0x00007fc435fd96db in start_thread (arg=0x7fc415ea6700) at
pthread_create.c:463
#6  0x00007fc430cc288f in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:95

Thread 2 (Thread 0x7fc4166a7700 (LWP 20469)):
#0  0x00007fc435fdf9f3 in futex_wait_cancelable (private=<optimized out>,
expected=0, futex_word=0x5602f3c31824) at
../sysdeps/unix/sysv/linux/futex-internal.h:88
#1  0x00007fc435fdf9f3 in __pthread_cond_wait_common (abstime=0x0,
mutex=0x5602f3c317d0, cond=0x5602f3c317f8) at pthread_cond_wait.c:502
#2  0x00007fc435fdf9f3 in __pthread_cond_wait (cond=0x5602f3c317f8,
mutex=0x5602f3c317d0) at pthread_cond_wait.c:655
#3  0x00007fc41b78bd5b in  () at /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
#4  0x00007fc41b78bbd7 in  () at /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
#5  0x00007fc435fd96db in start_thread (arg=0x7fc4166a7700) at
pthread_create.c:463
#6  0x00007fc430cc288f in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:95

Thread 1 (Thread 0x7fc4399c7bc0 (LWP 20451)):
#0  0x00007fc430c856c2 in __GI___waitpid (pid=20474, stat_loc=stat_loc
entry=0x7ffcf84ab3e8, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30
#1  0x00007fc430bf0067 in do_system (line=<optimized out>) at
../sysdeps/posix/system.c:149
#2  0x00007fc437e719fb in TUnixSystem::Exec(char const*)
(shellcmd=<optimized out>, this=0x5602f2796fb0) at
/home/gate/Softwares/root/core/unix/src/TUnixSystem.cxx:2119
#3  0x00007fc437e719fb in TUnixSystem::StackTrace() (this=0x5602f2796fb0)
at /home/gate/Softwares/root/core/unix/src/TUnixSystem.cxx:2413
#4  0x00007fc437e743e4 in TUnixSystem::DispatchSignals(ESignals)
(this=0x5602f2796fb0, sig=kSigSegmentationViolation) at
/home/gate/Softwares/root/core/unix/src/TUnixSystem.cxx:3644
#5  0x00007fc435fe4890 in <signal handler called> () at
/lib/x86_64-linux-gnu/libpthread.so.0
#6  0x00005602ef1aade5 in GateMaterialDatabase::~GateMaterialDatabase() ()
#7  0x00005602ef12d3e6 in
GateDetectorConstruction::~GateDetectorConstruction() ()
#8  0x00007fc43532c056 in G4RunManager::DeleteUserInitializations() () at
/usr/share/geant4/geant4.10.04.p02-install/lib/libG4run.so
#9  0x00007fc43532d250 in G4RunManager::~G4RunManager() () at
/usr/share/geant4/geant4.10.04.p02-install/lib/libG4run.so
#10 0x00005602ef6ac6d9 in GateRunManager::~GateRunManager() ()
#11 0x00005602ef0a43b5 in main ()
===========================================================


The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum http://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
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  0x00005602ef1aade5 in GateMaterialDatabase::~GateMaterialDatabase() ()
#7  0x00005602ef12d3e6 in
GateDetectorConstruction::~GateDetectorConstruction() ()
#8  0x00007fc43532c056 in G4RunManager::DeleteUserInitializations() () at
/usr/share/geant4/geant4.10.04.p02-install/lib/libG4run.so
#9  0x00007fc43532d250 in G4RunManager::~G4RunManager() () at
/usr/share/geant4/geant4.10.04.p02-install/lib/libG4run.so
#10 0x00005602ef6ac6d9 in GateRunManager::~GateRunManager() ()
#11 0x00005602ef0a43b5 in main ()
===========================================================
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