[Gate-users] Weird Phantom Warning

[Matthew Strugari]

Hi Xinjie,

It looks like you have issues with overlapping geometries. You could try nesting phantom4 within phantom3 and nest phantom3 within phantom2. Also, is the height of phantom3 correct at 800mm? This does not fit within your parent volume of phantom1.

Alternatively, is phantom3 even required? It looks like you’re reinserting polystyrene after voiding the region with air in phantom2. This could be avoided by setting Rmin to 2.4mm in phantom2.

Regards,
Matthew

From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> on behalf of Xinjie Cao <xinjie.cao at stonybrook.edu>
Date: Monday, January 18, 2021 at 12:38
To: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] Weird Phantom Warning
CAUTION: The Sender of this email is not from within Dalhousie.
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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