[Gate-users] Segmentation Violation

Josh Knowland jknowland at lucernodynamics.com
Wed Mar 30 18:34:16 CEST 2022 

All - an update on this segmentation violation. I realized that I was not getting the error on a VM running Ubuntu 20.04.4 LTS. So, for now, I'm just running on that. Still not sure what was causing it before.

-Josh

From: Josh Knowland
Sent: Tuesday, March 29, 2022 2:21 PM
To: gate-users <gate-users at lists.opengatecollaboration.org>
Subject: Segmentation Violation

Hello GATE users,

I am running into a segmentation violation error that seems to depend on material selection. I am simulating tubing with Y-90 in it. For some tubing materials, I get the following seg fault. If I make the tubing from Water, though, I get no error.
The virtual machine I'm using has multiple CPUs. It seems that I get no error if I run the same script on a VM with only one CPU.
The error seems to be while GATE is shutting down, so it doesn't appear to affect my simulation results.
I've run this type of simulation many times, so I have no idea what might have changed. Any ideas?



GATE output with error:


[G4]
[G4] **************************************************************
[G4]  Geant4 version Name: geant4-10-06-patch-01    (14-February-2020)
[G4]                        Copyright : Geant4 Collaboration
[G4]                       References : NIM A 506 (2003), 250-303
[G4]                                  : IEEE-TNS 53 (2006), 270-278
[G4]                                  : NIM A 835 (2016), 186-225
[G4]                              WWW : http://geant4.org/
[G4] **************************************************************
[G4]
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Core-0] Initialization of actors
[Core-0]
[Core-0] *************************************************
[Core-0]  GATE version 9.0 (March 2020)
[Core-0]  Copyright : OpenGATE Collaboration
[Core-0]  Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0]  Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0]  Reference : Med. Phys. 41(6)    (2014)
[Core-0]  http://www.opengatecollaboration.org
[Core-0] *************************************************
[Core-0]
[Core-0] You are using Geant4 version 10.6.1
[Core-0] Starting macro minsim_00.mac
0: RINDEX
1.84e-06   1.00028
4.08e-06   1.00028
9: GROUPVEL
1.84e-06   299.709
4.08e-06   299.709
14: ABSLENGTH
1.84e-06   50000
4.08e-06   50000
GateToTree::SetOutputIDName, id_system = '0' anOutputIDName = 'level1ID' depth = '1'
GateToTree::SetOutputIDName, id_system = '0' anOutputIDName = 'level2ID' depth = '2'
GateToTree::SetOutputIDName, id_system = '0' anOutputIDName = 'level3ID' depth = '3'
GateToTree::SetOutputIDName, id_system = '0' anOutputIDName = 'level4ID' depth = '4'
GateToTree::SetOutputIDName, id_system = '0' anOutputIDName = 'level5ID' depth = '5'
0: RINDEX
1e-06   1.33
5e-06   1.33
6e-06   1.33
7e-06   1.33
9: GROUPVEL
1e-06   225.408
3e-06   225.408
5.5e-06   225.408
7e-06   225.408
10: MIEHG
1e-06   2.3
5e-06   1.3
6e-06   3.2
7e-06   6.7
5: MIEHG_FORWARD
0.6
6: MIEHG_BACKWARD
0.6
7: MIEHG_FORWARD_RATIO
1
[Physic-0] The following Geant4's physic-list is enabled :emstandard
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
G4RadioactiveDecay is deprecated and will be removed in Geant4 version 11.
 Please replace it with G4RadioactiveDecayBase if you want the unbiased radioactive deacy process.
If you want the general process, with optional biasing, use G4Radioactivation.
[Core-0] Initialization of actors
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time   = 1 sec
[Acquisition-0] Simulation will have  = 1 run(s)
[Acquisition-0] Slice 0 from 0 to 1 s [slice=1 s]

### === G4UAtomicDeexcitation::InitialiseForNewRun()
=======================================================================
======       Radioactive Decay Physics Parameters              ========
=======================================================================
Max life time                                     1e+15 ps
Internal e- conversion flag                       1
Stored internal conversion coefficients           0
Enable correlated gamma emission                  0
Max 2J for sampling of angular correlations       10
Atomic de-excitation enabled                      1
Auger electron emission enabled                   1
Auger cascade enabled                             1
Check EM cuts disabled for atomic de-excitation   0
Use Bearden atomic level energies                 0
=======================================================================
G4VisManager: Using G4TrajectoryDrawByCharge as fallback trajectory model.
See commands in /vis/modeling/trajectories/ for other options.

### === G4UAtomicDeexcitation::InitialiseForNewRun()
[Core-0] End of macro minsim_00.mac
Graphics systems deleted.
Visualization Manager deleting...

*** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007f02c67a6337 in __GI___waitpid (pid=23991, stat_loc=stat_loc
entry=0x7ffdd5a86c68, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30
#1  0x00007f02c6711047 in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:149
#2  0x00007f02dff0da8b in TUnixSystem::StackTrace() () at /usr/share/cern/root-install/lib/libCore.so
#3  0x00007f02dff10474 in TUnixSystem::DispatchSignals(ESignals) () at /usr/share/cern/root-install/lib/libCore.so
#4  0x00007f02ceb4c980 in <signal handler called> () at /lib/x86_64-linux-gnu/libpthread.so.0
#5  0x000055fe1da2d820 in  ()
#6  0x000055fe180fe5b8 in GateMaterialDatabase::~GateMaterialDatabase() ()
#7  0x000055fe1807bee6 in GateDetectorConstruction::~GateDetectorConstruction() ()
#8  0x000055fe1807bf09 in GateDetectorConstruction::~GateDetectorConstruction() ()
#9  0x00007f02cde46ca6 in G4RunManager::DeleteUserInitializations() () at /usr/share/geant4/geant4-install/lib/libG4run.so
#10 0x00007f02cde47eb0 in G4RunManager::~G4RunManager() () at /usr/share/geant4/geant4-install/lib/libG4run.so
#11 0x000055fe18703079 in GateRunManager::~GateRunManager() ()
#12 0x000055fe17fc9778 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  0x000055fe1da2d820 in  ()
#6  0x000055fe180fe5b8 in GateMaterialDatabase::~GateMaterialDatabase() ()
#7  0x000055fe1807bee6 in GateDetectorConstruction::~GateDetectorConstruction() ()
#8  0x000055fe1807bf09 in GateDetectorConstruction::~GateDetectorConstruction() ()
#9  0x00007f02cde46ca6 in G4RunManager::DeleteUserInitializations() () at /usr/share/geant4/geant4-install/lib/libG4run.so
#10 0x00007f02cde47eb0 in G4RunManager::~G4RunManager() () at /usr/share/geant4/geant4-install/lib/libG4run.so
#11 0x000055fe18703079 in GateRunManager::~GateRunManager() ()
#12 0x000055fe17fc9778 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 !


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