[Gate-users] * Break * segmentation violation, vGATE8.1

Thu Jan 17 12:01:40 CET 2019

Hi,

You both (Andrew and Ashok) have reported a crash due to a "segmentation violation", but I'm afraid that theses crashes do not have the same cause. In the stack traces you can see that the crash happens in quite different parts of the source code. This by itself does not *exclude* that there is a single cause, but I think it's more likely that there are two independent subtle bugs (with not so subtle consequences).

Today I won't have time to look at this (reproduce the errors with a debugger). Hopefully tomorrow or next week.

/David

________________________________
Von: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> im Auftrag von GOSLING, Andrew (UNIVERSITY COLLEGE LONDON HOSPITALS NHS FOUNDATION TRUST) <andrew.gosling at nhs.net>
Gesendet: Donnerstag, 17. Jänner 2019 11:28:55
An: Ashok Tiwari; gate-users at lists.opengatecollaboration.org
Betreff: Re: [Gate-users] *** Break *** segmentation violation, vGATE8.1

I had this exact same issue, and raised a thread a week or so ago.  I only get this issue when trying to run GATE on a Raspberry Pi, but it's interesting that you are getting it too.  What kind of system are you using and which versions of the various software have you installed?

>From what I can find, the issue is to do with the dose actor interacting with the simulation.  From what I've been able to understand, the dose actor uses Root to sample the event list and convert the individual particle interactions into a more user-friendly output.  That is why your simulation runs fine, but will not produce any output.  I tried posting on the Root forum but they claimed it was a GATE problem, and my thread here went quiet after the initial reply.

My first suggestion would be to check your Root installation is working, beyond that I am in the same boat as you.

Andrew

Andrew Gosling (DPhil)     |     Clinical Scientist (Proton Beam Physics)
UCLH Radiotherapy Physics, 1st Floor East, 250 Euston Road, London, NW1 2PG
andrew.gosling at nhs.net     |     +44 (0) 203 44 72490

-----Original Message-----
From: Ashok Tiwari [mailto:tiwarias at yahoo.com]
Sent: 16 January 2019 17:58
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] *** Break *** segmentation violation, vGATE8.1

Dear community,

I’m using vGATE8.1 for my simulation. When I ran a simulation, visualization of simulations looks ok, but at the very end of the simulation I‘m having break segmentation violation. Can anyone tell me what might be the causes of it? Following lines are copy-paste of what I’m seeing:

Visualization Manager deleting...
G4 kernel has come to Quit state.

 *** Break *** segmentation violation
===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007f161fdc8687 in __GI___waitpid (pid=4437, stat_loc=stat_loc
entry=0x7fff4f1b4228, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30
#1  0x00007f161fd33067 in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:149
#2  0x00007f1626fb49fb in TUnixSystem::Exec(char const*) (shellcmd=<optimized out>, this=0x5628cd1c2fb0) at /home/gate/Softwares/root/core/unix/src/TUnixSystem.cxx:2119
#3  0x00007f1626fb49fb in TUnixSystem::StackTrace() (this=0x5628cd1c2fb0) at /home/gate/Softwares/root/core/unix/src/TUnixSystem.cxx:2413
#4  0x00007f1626fb73e4 in TUnixSystem::DispatchSignals(ESignals) (this=0x5628cd1c2fb0, sig=kSigSegmentationViolation) at /home/gate/Softwares/root/core/unix/src/TUnixSystem.cxx:3644
#5  0x00007f1625127890 in <signal handler called> () at /lib/x86_64-linux-gnu/libpthread.so.0
#6  0x00005628d150db30 in  ()
#7  0x00005628ca58cde8 in GateMaterialDatabase::~GateMaterialDatabase() ()
#8  0x00005628ca50f3e6 in GateDetectorConstruction::~GateDetectorConstruction() ()
#9  0x00007f162446f056 in G4RunManager::DeleteUserInitializations() () at /usr/share/geant4/geant4.10.04.p02-install/lib/libG4run.so
#10 0x00007f1624470250 in G4RunManager::~G4RunManager() () at /usr/share/geant4/geant4.10.04.p02-install/lib/libG4run.so
#11 0x00005628caa8e6d9 in GateRunManager::~GateRunManager() ()
#12 0x00005628ca4863b5 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.
===========================================================
#6  0x00005628d150db30 in  ()
#7  0x00005628ca58cde8 in GateMaterialDatabase::~GateMaterialDatabase() ()
#8  0x00005628ca50f3e6 in GateDetectorConstruction::~GateDetectorConstruction() ()
#9  0x00007f162446f056 in G4RunManager::DeleteUserInitializations() () at /usr/share/geant4/geant4.10.04.p02-install/lib/libG4run.so
#10 0x00007f1624470250 in G4RunManager::~G4RunManager() () at /usr/share/geant4/geant4.10.04.p02-install/lib/libG4run.so
#11 0x00005628caa8e6d9 in GateRunManager::~GateRunManager() ()
#12 0x00005628ca4863b5 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 !

Regards,
Ashok

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