[Gate-users] Weird Phantom Warning
Xinjie Cao
xinjie.cao at stonybrook.edu
Mon Jan 18 17:54:59 CET 2021
Hi Gefei,
Thanks for your reply! I think it makes sense.
PS: 谢谢！
Best,
On Mon, Jan 18, 2021 at 11:51 AM 陈戈飞 <seucgf at gmail.com> wrote:
> 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
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
--
*....................................................*
*Xinjie Cao*
*M.E. / Ph.D. Candidate*
*Research Project Assistant*
*Department of Electrical and Computer Engineering & Radiology *
*Novel Medical Imaging Technologies Lab*
*Health Science Center Level 8*
*Stony Brook, NY 11794-8460 *
*Tel: +1 (631)202-9445*
you.stonybrook.edu/goldan/people/
*email: **xinjie.cao at stonybroo*k.edu <xinjie.cao at stonybrook.edu>
*....................................................*
It is prohibited to distribute or publish the files attached to any other
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