[Gate-users] Simulations terminate after a few hours with cryptic errors
Träuble, Korbinian Linus
korbinian.traeuble at tum.de
Wed Sep 21 11:39:50 CEST 2022
Dear all,
I’m facing some cryptic error messages in my GATE simulations. I always get some after the macro ends, but still get the desired result. So I’ve just ignored it. It normally looks like this:
2022-09-18 12:33:15 UTC -- Run terminated.
2022-09-18 12:33:15 UTC -- Run Summary
2022-09-18 12:33:15 UTC -- Run Aborted after 1166176513 events processed.
2022-09-18 12:33:15 UTC -- User=15012.720000s Real=15049.712099s Sys=0.570000s
2022-09-18 12:33:15 UTC -- 0 events have been kept for refreshing and/or reviewing.
2022-09-18 12:33:15 UTC -- "/vis/reviewKeptEvents" to review them one by one.
2022-09-18 12:33:15 UTC -- "/vis/enable", then "/vis/viewer/flush" or "/vis/viewer/rebuild" to see them accumulated.
2022-09-18 12:33:15 UTC -- [Core-0] End of macro mac/Main_Thyroid.mac
2022-09-18 12:33:15 UTC -- Graphics systems deleted.
2022-09-18 12:33:15 UTC -- Visualization Manager deleting...
2022-09-18 12:33:15 UTC -- G4 kernel has come to Quit state.
2022-09-18 12:33:15 UTC --
2022-09-18 12:33:15 UTC -- ### CAUGHT SIGNAL: 11 ### address: 0, signal = SIGSEGV, value = 11, description = segmentation violation. Unknown segmentation fault error: 128.
2022-09-18 12:33:15 UTC --
2022-09-18 12:33:15 UTC -- Backtrace:
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][0/9]> Gate() [0x9cf985]
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][1/9]> Gate() [0x96d45e]
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][2/9]> Gate() [0x96d479]
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][3/9]> /software/geant4/install/lib64/libG4run.so(_ZN12G4RunManager25DeleteUserInitializationsEv+0x16) [0x7f4983ee8e76]
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][4/9]> /software/geant4/install/lib64/libG4run.so(_ZN12G4RunManagerD1Ev+0xd5) [0x7f4983ee9af5]
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][5/9]> Gate() [0x92c5c9]
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][6/9]> Gate() [0x4dd044]
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][7/9]> /usr/lib64/libc.so.6(__libc_start_main+0xf3) [0x7f4979b50493]
2022-09-18 12:33:15 UTC -- [PID=64, TID=-2][8/9]> Gate() [0x53bf0e]
2022-09-18 12:33:15 UTC --
2022-09-18 12:33:15 UTC -- : Segmentation fault (Signal sent by the kernel [(nil)])
But currently I’m facing the problem that my simulation run perfectly fine until it terminates after 91s (7 hours in real time) of 300s with the following error message and I don’t get a result. I also don’t know why its starting again to print the table of registered couples. For these simulations I’m using a 23MBq mono energetic 140keV gamma source.
2022-09-20 16:10:16 UTC -- Run terminated.
2022-09-20 16:10:16 UTC -- Run Summary
2022-09-20 16:10:16 UTC -- Number of events processed : 2147483647
2022-09-20 16:10:16 UTC -- User=26376.230000s Real=26453.022547s Sys=0.910000s
2022-09-20 16:10:16 UTC -- 0 events have been kept for refreshing and/or reviewing.
2022-09-20 16:10:16 UTC -- "/vis/reviewKeptEvents" to review them one by one.
2022-09-20 16:10:16 UTC -- "/vis/enable", then "/vis/viewer/flush" or "/vis/viewer/rebuild" to see them accumulated.
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- ### CAUGHT SIGNAL: 11 ### address: 0x5f8, signal = SIGSEGV, value = 11, description = segmentation violation. Address not mapped to object.
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- ========= Table of registered couples ============================
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- Index : 0 used in the geometry : Yes
2022-09-20 16:10:16 UTC -- Material : Air
2022-09-20 16:10:16 UTC -- Range cuts : gamma 1 mm e- 1 mm e+ 1 mm proton 1 mm
2022-09-20 16:10:16 UTC -- Energy thresholds : gamma 1 keV e- 1 keV e+ 1 keV proton 100 keV
2022-09-20 16:10:16 UTC -- Region(s) which use this couple :
2022-09-20 16:10:16 UTC -- DefaultRegionForTheWorld
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- Index : 1 used in the geometry : Yes
2022-09-20 16:10:16 UTC -- Material : Air
2022-09-20 16:10:16 UTC -- Range cuts : gamma 1 mm e- 1 mm e+ 1 mm proton 1 mm
2022-09-20 16:10:16 UTC -- Energy thresholds : gamma 1 keV e- 1 keV e+ 1 keV proton 100 keV
2022-09-20 16:10:16 UTC -- Region(s) which use this couple :
2022-09-20 16:10:16 UTC -- SPECThead
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- Index : 2 used in the geometry : Yes
2022-09-20 16:10:16 UTC -- Material : Air
2022-09-20 16:10:16 UTC -- Range cuts : gamma 1 mm e- 1 mm e+ 1 mm proton 1 mm
2022-09-20 16:10:16 UTC -- Energy thresholds : gamma 1 keV e- 1 keV e+ 1 keV proton 100 keV
2022-09-20 16:10:16 UTC -- Region(s) which use this couple :
2022-09-20 16:10:16 UTC -- cover
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- Backtrace:
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 0/20]> Gate() [0x6395ba]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 1/20]> Gate() [0x55c4a0]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 2/20]> Gate() [0x860c22]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 3/20]> Gate() [0x551e85]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 4/20]> /software/geant4/install/lib64/libG4run.so(_ZN12G4RunManager17RunInitializationEv+0x474) [0x7fa76a3ad604]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 5/20]> Gate() [0x92ebcd]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 6/20]> /software/geant4/install/lib64/libG4run.so(_ZN12G4RunManager6BeamOnEiPKci+0x4d) [0x7fa76a3a860d]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 7/20]> Gate() [0x8b649d]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 8/20]> Gate() [0x8bb4a8]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][ 9/20]> /software/geant4/install/lib64/libG4intercoms.so(_ZN11G4UIcommand4DoItE8G4String+0x33c) [0x7fa766151a3c]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][10/20]> /software/geant4/install/lib64/libG4intercoms.so(_ZN11G4UImanager12ApplyCommandEPKc+0x682) [0x7fa7661696c2]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][11/20]> /software/geant4/install/lib64/libG4intercoms.so(_ZN9G4UIbatch11ExecCommandERK8G4String+0x17) [0x7fa766141807]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][12/20]> /software/geant4/install/lib64/libG4intercoms.so(_ZN9G4UIbatch12SessionStartEv+0x75) [0x7fa766142835]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][13/20]> /software/geant4/install/lib64/libG4intercoms.so(_ZN11G4UImanager16ExecuteMacroFileEPKc+0x3c) [0x7fa76616ae0c]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][14/20]> /software/geant4/install/lib64/libG4intercoms.so(_ZN20G4UIcontrolMessenger11SetNewValueEP11G4UIcommand8G4String+0x23b) [0x7fa76615eafb]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][15/20]> /software/geant4/install/lib64/libG4intercoms.so(_ZN11G4UIcommand4DoItE8G4String+0x33c) [0x7fa766151a3c]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][16/20]> /software/geant4/install/lib64/libG4intercoms.so(_ZN11G4UImanager12ApplyCommandEPKc+0x682) [0x7fa7661696c2]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][17/20]> Gate() [0x4dd569]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][18/20]> /usr/lib64/libc.so.6(__libc_start_main+0xf3) [0x7fa760010493]
2022-09-20 16:10:16 UTC -- [PID=64, TID=-2][19/20]> Gate() [0x53bf0e]
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- : Segmentation fault (Address not mapped to object [0x5f8])
2022-09-20 16:10:16 UTC -- Index : 3 used in the geometry : Yes
2022-09-20 16:10:16 UTC -- Material : Air
2022-09-20 16:10:16 UTC -- Range cuts : gamma 1 mm e- 1 mm e+ 1 mm proton 1 mm
2022-09-20 16:10:16 UTC -- Energy thresholds : gamma 1 keV e- 1 keV e+ 1 keV proton 100 keV
2022-09-20 16:10:16 UTC -- Region(s) which use this couple :
2022-09-20 16:10:16 UTC -- cover2
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- Index : 4 used in the geometry : Yes
2022-09-20 16:10:16 UTC -- Material : NaITl
2022-09-20 16:10:16 UTC -- Range cuts : gamma 1 mm e- 1 mm e+ 1 mm proton 1 mm
2022-09-20 16:10:16 UTC -- Energy thresholds : gamma 30.2503 keV e- 620.21 keV e+ 591.843 keV proton 100 keV
2022-09-20 16:10:16 UTC -- Region(s) which use this couple :
2022-09-20 16:10:16 UTC -- crystal
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- Index : 5 used in the geometry : Yes
2022-09-20 16:10:16 UTC -- Material : Lead
2022-09-20 16:10:16 UTC -- Range cuts : gamma 1 mm e- 1 mm e+ 1 mm proton 1 mm
2022-09-20 16:10:16 UTC -- Energy thresholds : gamma 101.898 keV e- 1.37707 MeV e+ 1.28764 MeV proton 100 keV
2022-09-20 16:10:16 UTC -- Region(s) which use this couple :
2022-09-20 16:10:16 UTC -- collimator
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- Index : 6 used in the geometry : Yes
2022-09-20 16:10:16 UTC -- Material : Air
2022-09-20 16:10:16 UTC -- Range cuts : gamma 1 mm e- 1 mm e+ 1 mm proton 1 mm
2022-09-20 16:10:16 UTC -- Energy thresholds : gamma 1 keV e- 1 keV e+ 1 keV proton 100 keV
2022-09-20 16:10:16 UTC -- Region(s) which use this couple :
2022-09-20 16:10:16 UTC -- hole1
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- Index : 7 used in the geometry : Yes
2022-09-20 16:10:16 UTC -- Material : Water
2022-09-20 16:10:16 UTC -- Range cuts : gamma 1 mm e- 1 mm e+ 1 mm proton 1 mm
2022-09-20 16:10:16 UTC -- Energy thresholds : gamma 2.93516 keV e- 351.296 keV e+ 341.588 keV proton 100 keV
2022-09-20 16:10:16 UTC -- Region(s) which use this couple :
2022-09-20 16:10:16 UTC -- box2
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- ==================================================================
2022-09-20 16:10:16 UTC --
2022-09-20 16:10:16 UTC -- ### Run 0 starts.
I’m using the opengatecollaboration/gate:latest docker image and it runs on a Polyaxon cluster. Is this a GATE problem and does anybody know how to solve it?
Kind regards,
Korbinian
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