[Gate-users] Segmentation Violation

David Sarrut david.sarrut at creatis.insa-lyon.fr
Wed Mar 30 20:06:16 CEST 2022 

Hi Josh,

maybe try to upgrade to 9.2 (with G4 v11)?

cheers,
David

On Wed, Mar 30, 2022 at 6:34 PM Josh Knowland <jknowland at lucernodynamics.com>
wrote:

> 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 !
>
>
>
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users



-- 
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U1294
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://dsarrut.github.io
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
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