[Gate-users] Weird Phantom Warning

[Xinjie Cao]

Dear GATE users,

I am simulating the count rate performance of some PET scanners, while I
found an interesting warning/error when I made a change to the phantom
configuration.

*With the following simplified phantom configuration, both single thread or
cluster tool can run the macro well:*
#==========================
#  P H A N T O M
#==========================

/gate/world/daughters/name phantom1
/gate/world/daughters/insert cylinder
/gate/phantom1/placement/setTranslation           0.0 0.0 0.0 mm
/gate/phantom1/geometry/setRmax                   101.5 mm
/gate/phantom1/geometry/setHeight                 700 mm
/gate/phantom1/setMaterial                        Polyethylene
/gate/phantom1/attachPhantomSD

/gate/phantom1/daughters/name phantom2
/gate/phantom1/daughters/insert cylinder
/gate/phantom2/placement/setTranslation           0.0 -45.0 0.0 mm
/gate/phantom2/geometry/setRmax                   3.2 mm
/gate/phantom2/geometry/setHeight                 700 mm
/gate/phantom2/setMaterial                        Air
/gate/phantom2/attachPhantomSD

*While when I added two more daughter phantoms inside the previous outer
shell volume as followed*,

#===========================
#  P H A N T O M
#===========================

/gate/world/daughters/name phantom1
/gate/world/daughters/insert cylinder
/gate/phantom1/placement/setTranslation           0.0 0.0 0.0 mm
/gate/phantom1/geometry/setRmax                   101.5 mm
/gate/phantom1/geometry/setHeight                 700 mm
/gate/phantom1/setMaterial                        Polyethylene
/gate/phantom1/attachPhantomSD

/gate/phantom1/daughters/name phantom2
/gate/phantom1/daughters/insert cylinder
/gate/phantom2/placement/setTranslation           0.0 -45.0 0.0 mm
/gate/phantom2/geometry/setRmax                   3.2 mm
/gate/phantom2/geometry/setHeight                 700 mm
/gate/phantom2/setMaterial                        Air
/gate/phantom2/attachPhantomSD

/gate/phantom1/daughters/name phantom3
/gate/phantom1/daughters/insert cylinder
/gate/phantom3/placement/setTranslation           0.0 -45.0 0.0 mm
/gate/phantom3/geometry/setRmax                   2.4 mm
/gate/phantom3/geometry/setRmin                   1.6 mm
/gate/phantom3/geometry/setHeight                 800 mm
/gate/phantom3/setMaterial                        Polyethylene
/gate/phantom3/attachPhantomSD

/gate/phantom1/daughters/name phantom4
/gate/phantom1/daughters/insert cylinder
/gate/phantom4/placement/setTranslation           0.0 -45.0 0.0 mm
/gate/phantom4/geometry/setRmax                   1.6 mm
/gate/phantom4/geometry/setHeight                 700 mm
/gate/phantom4/setMaterial                        Water
/gate/phantom4/attachPhantomSD

*the GATE feedbacked a warning/error like this,*

*** Break *** segmentation violation

===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007f563c6d146c in waitpid () at /lib64/libc.so.6
#1  0x00007f563c64ef62 in do_system () at /lib64/libc.so.6
#2  0x00007f564b4c70c4 in TUnixSystem::StackTrace() () at
/home/goldan/GATE/root/lib/libCore.so.6.18
#3  0x00007f564b4c97fc in TUnixSystem::DispatchSignals(ESignals) () at
/home/goldan/GATE/root/lib/libCore.so.6.18
#4  0x00007f56471f4630 in <signal handler called> () at
/lib64/libpthread.so.0
#5  0x0000000000000040 in  ()
#6  0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()
#7  0x000000000087a8e6 in
GateDetectorConstruction::~GateDetectorConstruction() ()
#8  0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations()
(this=this
entry=0x32997c0) at
/home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236
#9  0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0,
__in_chrg=<optimized out>) at
/home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211
#10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()
#11 0x000000000050198f 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.
===========================================================
#5  0x0000000000000040 in  ()
#6  0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()
#7  0x000000000087a8e6 in
GateDetectorConstruction::~GateDetectorConstruction() ()
#8  0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations()
(this=this
entry=0x32997c0) at
/home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236
#9  0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0,
__in_chrg=<optimized out>) at
/home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211
#10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()
#11 0x000000000050198f in main ()
===========================================================


WARNING - Attempt to delete the physical volume store while geometry closed
!
WARNING - Attempt to delete the logical volume store while geometry closed !
WARNING - Attempt to delete the solid store while geometry closed !
WARNING - Attempt to delete the region store while geometry closed !

*The cluster tool could run the macro with added phantom configuration well
with no warning/error, so I am not sure where the wrong with it or whether
it has an* *influence on the simulation result. I probably have seen *a*
similar issue when I used CASToR for reconstruction so I am guessing it is
related to ROOT?*

*Did anyone ever meet this issue before? Any reply will be highly
appreciated! Thanks!*

Best,
Xinjie
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