[Gate-users] gate crash when repeating in z direction
tstoole
tstoole at zoho.com
Thu Apr 26 16:51:30 CEST 2018
Hi,
I am running vGate 8.0. I am getting a crash when I try to
repeat a pixel into the z direction. I am able to reproduce the
crash when running a slightly modified GateContrib/imaging/CT/classic/benchmarkCT.
I can run the original classic/benchmarkCT successfully. However, if
the CTScanner.mac file is modified to the one appended below,
Gate crashes. The output from the crash is also appended below.
I get the same results if I comment out the phantom call from benchmarkCT.mac.
I don't think that any of the geometry is overlapping. But something is
not right. Does anyone have any thoughts or suggestions on
what the problem is?
Thanks in advance for your help,
Terry
Here is the world geometry that is being used.
/gate/world/geometry/setXLength 50. cm
/gate/world/geometry/setYLength 50. cm
/gate/world/geometry/setZLength 50. cm
Here is my modified version of CTScanner.mac. Original lines have
been commented out where changes have been made.
####################
# CTscanner system #
####################
/gate/world/daughters/name CTscanner
/gate/world/daughters/insert box
/gate/CTscanner/placement/setTranslation 0. 0. 150.5 mm
/gate/CTscanner/geometry/setXLength 50. mm
/gate/CTscanner/geometry/setYLength 50. mm
#/gate/CTscanner/geometry/setZLength 1. mm
/gate/CTscanner/geometry/setZLength 20. mm
/gate/CTscanner/setMaterial Air
/gate/CTscanner/vis/forceWireframe
/gate/CTscanner/vis/setColor white
############# ############
# CTSCANNER # ----> # MODULE #
############# ############
/gate/CTscanner/daughters/name module
/gate/CTscanner/daughters/insert box
/gate/module/geometry/setXLength 50. mm
/gate/module/geometry/setYLength 50. mm
#/gate/module/geometry/setZLength 1. mm
/gate/module/geometry/setZLength 20. mm
/gate/module/setMaterial Silicon
/gate/module/vis/forceWireframe
/gate/module/vis/setColor white
############ #############
# MODULE # ----> # CLUSTER_0 #
############ #############
/gate/module/daughters/name cluster
/gate/module/daughters/insert box
/gate/cluster/geometry/setXLength 50. mm
/gate/cluster/geometry/setYLength 50. mm
#/gate/cluster/geometry/setZLength 1. mm
/gate/cluster/geometry/setZLength 20. mm
/gate/cluster/setMaterial Air
/gate/cluster/vis/forceWireframe
/gate/cluster/vis/setColor white
############ ############# ###########
# MODULE # ----> # CLUSTER_0 # ----> # PIXEL_0 #
############ ############# ###########
/gate/cluster/daughters/name pixel
/gate/cluster/daughters/insert box
/gate/pixel/geometry/setXLength 0.5 mm
/gate/pixel/geometry/setYLength 0.5 mm
/gate/pixel/geometry/setZLength 1. mm
/gate/pixel/setMaterial Silicon
/gate/pixel/vis/setColor red
# REPEAT PIXEl_0
/gate/pixel/repeaters/insert cubicArray
/gate/pixel/cubicArray/setRepeatNumberX 100
/gate/pixel/cubicArray/setRepeatNumberY 100
/gate/pixel/cubicArray/setRepeatNumberZ 20
#/gate/pixel/cubicArray/setRepeatNumberZ 1
#/gate/pixel/cubicArray/setRepeatVector 0.5 0.5 0.00 mm
/gate/pixel/cubicArray/setRepeatVector 0.5 0.5 1.00 mm
/gate/pixel/cubicArray/autoCenter true
# ATTACH SYSTEM
/gate/systems/CTscanner/module/attach module
/gate/systems/CTscanner/cluster_0/attach cluster
/gate/systems/CTscanner/pixel_0/attach pixel
# ATTACH LAYER
/gate/pixel/attachCrystalSD
[145] 16:17 vgate:~/GateContrib/imaging/CT/test2 > Gate benchmarkCT.mac
[G4]
[G4] *************************************************************
[G4] Geant4 version Name: geant4-10-03-patch-03 (20-October-2017)
[G4] Copyright : Geant4 Collaboration
[G4] Reference : NIM A 506 (2003), 250-303
[G4] WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4]
[G4] ### WARNING: G4EmProcessOptions class is obsolete and will be removed in the next public release
Please, try to use G4EmParameters class and/or UI interface to EM parameters
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[G4] ### WARNING: G4EmProcessOptions class is obsolete and will be removed in the next public release
Please, try to use G4EmParameters class and/or UI interface to EM parameters
[Core-0] Initialization of actors
[Core-0]
[Core-0] **********************************************************************
[Core-0] GATE version name: gate_v8.0
[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 Geant4 version 10.3.3
[Core-0] Starting macro benchmarkCT.mac
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Rmin/gate/aluminiumBall/geometry/setRmin
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Rmin/gate/PVCBall/geometry/setRmin
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Rmin/gate/glassBall/geometry/setRmin
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Rmin/gate/spineBoneBall/geometry/setRmin
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
<!> *** WARNING *** <!> Unknown process: MultipleScattering
List of Enabled processes:
=== Process: PhotoElectric ===
Particle: gamma
* Model(s):
- StandardModel
=== Process: Compton ===
Particle: gamma
* Model(s):
- PenelopeModel
=== Process: RayleighScattering ===
Particle: gamma
* Model(s):
- PenelopeModel
=== Process: Bremsstrahlung ===
Particle: e+
* Model(s):
- <!> *** Warning *** <!> No model selected!
Particle: e-
* Model(s):
- StandardModel
=== Process: ElectronIonisation ===
Particle: e+
* Model(s):
- <!> *** Warning *** <!> No model selected!
Particle: e-
* Model(s):
- StandardModel
List of initialized processes:
[Core-0] Initialization of geometry
[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
### WARNING: G4EmProcessOptions class is obsolete and will be removed in the next public release
Please, try to use G4EmParameters class and/or UI interface to EM parameters
[Core-0] Initialization of actors
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
----------------------
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time = 10 sec
[Acquisition-0] Simulation will have = 1 run(s)
****
Number of Pixels in your detector : 200000
Number of bytes by projection : 781.25 Kb
****
[Acquisition-0] Slice 0 from 0 to 10 s [slice=10 s]
WARNING from G4PenelopeComptonModel
Atomic de-excitation module is not instantiated, so there will not be any fluorescence/Auger emission.
Please make sure this is intended
PhotoElectric: for gamma, applyCuts: 1 SubType= 12 BuildTable= 0
LambdaPrime table from 200 keV to 100 TeV in 61 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
PhotoElectric : Emin= 0 eV Emax= 100 TeV AngularGenSauterGavrila
Compton: for gamma, applyCuts: 1 SubType= 13 BuildTable= 1
Lambda table from 100 eV to 1 MeV, 7 bins per decade, spline: 1
LambdaPrime table from 1 MeV to 100 TeV in 56 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
PenCompton : Emin= 0 eV Emax= 100 TeV
RayleighScattering: for gamma, applyCuts: 1 SubType= 11 BuildTable= 1
Lambda table from 100 eV to 100 keV, 7 bins per decade, spline: 0
LambdaPrime table from 100 keV to 100 TeV in 63 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
PenRayleigh : Emin= 0 eV Emax= 100 GeV
Bremsstrahlung: for e- SubType= 3
dE/dx and range tables from 100 eV to 100 TeV in 84 bins
Lambda tables from threshold to 100 TeV, 7 bins per decade, spline: 1
LPM flag: 1 for E > 1 GeV, VertexHighEnergyTh(GeV)= 100000
===== EM models for the G4Region DefaultRegionForTheWorld ======
eBremSB : Emin= 0 eV Emax= 1 GeV DipBustGen
eBremLPM : Emin= 1 GeV Emax= 100 TeV DipBustGen
ElectronIonisation: for e- SubType= 2
dE/dx and range tables from 100 eV to 100 TeV in 84 bins
Lambda tables from threshold to 100 TeV, 7 bins per decade, spline: 1
finalRange(mm)= 1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
MollerBhabha : Emin= 0 eV Emax= 100 TeV
Bremsstrahlung: for e+ SubType= 3
dE/dx and range tables from 100 eV to 100 TeV in 84 bins
Lambda tables from threshold to 100 TeV, 7 bins per decade, spline: 1
LPM flag: 1 for E > 1 GeV, VertexHighEnergyTh(GeV)= 100000
===== EM models for the G4Region DefaultRegionForTheWorld ======
eBremSB : Emin= 0 eV Emax= 1 GeV DipBustGen
eBremLPM : Emin= 1 GeV Emax= 100 TeV DipBustGen
ElectronIonisation: for e+ SubType= 2
dE/dx and range tables from 100 eV to 100 TeV in 84 bins
Lambda tables from threshold to 100 TeV, 7 bins per decade, spline: 1
finalRange(mm)= 1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
MollerBhabha : Emin= 0 eV Emax= 100 TeV
*** Break *** segmentation violation
===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0 0x00007fd2276bd07a in __GI___waitpid (pid=10280, stat_loc=stat_loc
entry=0x7fff3d34a840, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
#1 0x00007fd227635fbb in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:148
#2 0x00007fd22fc63dd4 in TUnixSystem::StackTrace() () from /usr/lib/x86_64-linux-gnu/libCore.so.5.34
#3 0x00007fd22fc6603c in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib/x86_64-linux-gnu/libCore.so.5.34
#4 <signal handler called>
#5 0x00007fd22ea9c154 in TBranch::GetBasket(int) () from /usr/lib/x86_64-linux-gnu/libTree.so.5.34
#6 0x00007fd22ea9d90b in TBranch::Fill() () from /usr/lib/x86_64-linux-gnu/libTree.so.5.34
#7 0x00007fd22ea86851 in TTree::Fill() () from /usr/lib/x86_64-linux-gnu/libTree.so.5.34
#8 0x0000000000796154 in GateToRoot::SingleOutputChannel::RecordDigitizer() ()
#9 0x0000000000795c6e in GateToRoot::RecordEndOfEvent(G4Event const*) ()
#10 0x00000000008a85a7 in GateOutputMgr::RecordEndOfEvent(G4Event const*) ()
#11 0x000000000091f369 in GateEventAction::EndOfEventAction(G4Event const*) ()
#12 0x00007fd22bf12927 in G4EventManager::DoProcessing(G4Event*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4event.so
#13 0x00007fd22c1a6915 in G4RunManager::ProcessOneEvent(int) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4run.so
#14 0x00007fd22c1a4943 in G4RunManager::DoEventLoop(int, char const*, int) [clone .localalias.94] () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4run.so
#15 0x00007fd22c1a4b7b in G4RunManager::BeamOn(int, char const*, int) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4run.so
#16 0x0000000000b0578c in GateApplicationMgr::StartDAQ() ()
#17 0x0000000000a99a20 in GateApplicationMgrMessenger::SetNewValue(G4UIcommand*, G4String) ()
#18 0x00007fd228982e0c in G4UIcommand::DoIt(G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#19 0x00007fd22899f018 in G4UImanager::ApplyCommand(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#20 0x00007fd22896cc57 in G4UIbatch::ExecCommand(G4String const&) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#21 0x00007fd22896ea2e in G4UIbatch::SessionStart() () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#22 0x00007fd22899fd32 in G4UImanager::ExecuteMacroFile(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#23 0x00007fd22898d499 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#24 0x00007fd228982e0c in G4UIcommand::DoIt(G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#25 0x00007fd22899f018 in G4UImanager::ApplyCommand(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#26 0x00007fd22896cc57 in G4UIbatch::ExecCommand(G4String const&) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#27 0x00007fd22896ea2e in G4UIbatch::SessionStart() () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#28 0x00007fd22899fd32 in G4UImanager::ExecuteMacroFile(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#29 0x00007fd22898d499 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#30 0x00007fd228982e0c in G4UIcommand::DoIt(G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#31 0x00007fd22899f018 in G4UImanager::ApplyCommand(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#32 0x000000000054785e 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 0x00007fd22ea9c154 in TBranch::GetBasket(int) () from /usr/lib/x86_64-linux-gnu/libTree.so.5.34
#6 0x00007fd22ea9d90b in TBranch::Fill() () from /usr/lib/x86_64-linux-gnu/libTree.so.5.34
#7 0x00007fd22ea86851 in TTree::Fill() () from /usr/lib/x86_64-linux-gnu/libTree.so.5.34
#8 0x0000000000796154 in GateToRoot::SingleOutputChannel::RecordDigitizer() ()
#9 0x0000000000795c6e in GateToRoot::RecordEndOfEvent(G4Event const*) ()
#10 0x00000000008a85a7 in GateOutputMgr::RecordEndOfEvent(G4Event const*) ()
#11 0x000000000091f369 in GateEventAction::EndOfEventAction(G4Event const*) ()
#12 0x00007fd22bf12927 in G4EventManager::DoProcessing(G4Event*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4event.so
#13 0x00007fd22c1a6915 in G4RunManager::ProcessOneEvent(int) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4run.so
#14 0x00007fd22c1a4943 in G4RunManager::DoEventLoop(int, char const*, int) [clone .localalias.94] () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4run.so
#15 0x00007fd22c1a4b7b in G4RunManager::BeamOn(int, char const*, int) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4run.so
#16 0x0000000000b0578c in GateApplicationMgr::StartDAQ() ()
#17 0x0000000000a99a20 in GateApplicationMgrMessenger::SetNewValue(G4UIcommand*, G4String) ()
#18 0x00007fd228982e0c in G4UIcommand::DoIt(G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#19 0x00007fd22899f018 in G4UImanager::ApplyCommand(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#20 0x00007fd22896cc57 in G4UIbatch::ExecCommand(G4String const&) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#21 0x00007fd22896ea2e in G4UIbatch::SessionStart() () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#22 0x00007fd22899fd32 in G4UImanager::ExecuteMacroFile(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#23 0x00007fd22898d499 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#24 0x00007fd228982e0c in G4UIcommand::DoIt(G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#25 0x00007fd22899f018 in G4UImanager::ApplyCommand(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#26 0x00007fd22896cc57 in G4UIbatch::ExecCommand(G4String const&) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#27 0x00007fd22896ea2e in G4UIbatch::SessionStart() () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#28 0x00007fd22899fd32 in G4UImanager::ExecuteMacroFile(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#29 0x00007fd22898d499 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#30 0x00007fd228982e0c in G4UIcommand::DoIt(G4String) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#31 0x00007fd22899f018 in G4UImanager::ApplyCommand(char const*) () from /usr/share/geant4/geant4.10.03.p03-install/lib/libG4intercoms.so
#32 0x000000000054785e in main ()
===========================================================
Segmentation fault (core dumped)
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