[Gate-users] Weird Phantom Warning
陈戈飞
seucgf at gmail.com
Mon Jan 18 17:50:51 CET 2021
You don't have enough ram.
It appears when not enough memory available for new array.
Xinjie Cao <xinjie.cao at stonybrook.edu>于2021年1月19日 周二00:38写道：
> 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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> Gate-users at lists.opengatecollaboration.org
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