[Gate-users] Simulation crashes unexpectedly

Wed Feb 3 08:44:27 CET 2021

Hello,

thanks for the information. The feedback from Cassandra scares me a bit ;)
As DavidB said, could you try to have a minimal example with the latest
version of Gate (develop branch from the github + G4 10.7) ?
My two cents guess is it may be an issue during the digitization process
for SPECT that involve root output.

thanks
David

On Wed, Feb 3, 2021 at 12:09 AM David Boersma <david.boersma at acmit.at>
wrote:

> Hi Matthew and Cassandra,
>
> Segfaults are embarrassing and should be fixed. The backtrace sometimes
> helps, but I didn't see any clear hints in the one you provided. In order
> to have a chance to solve it we'd need a minimal Gate macro that enables us
> to reproduce this problem. Use a fixed seed and tell us after how long it
> runs before it crashes for you. It can sometimes help if in addition the
> versions of Gate, Geant4 and ROOT, you also specify which OS (name and
> release), which compiler and some specs of the hardware you run it on.
> Please post all these details in a GitHub #issue so that it won't get
> buried in history.
>
> Debugging this sort of problems is very necessary (because they are so
> embarrassing!), but it is also hard and time consuming (run it under
> "valgrind" and study the very verbose logs), so I don't guarantee that it
> will be fixed any time soon, even if we have a GitHub #issue with the full
> information. Sorry for the inconvenience!
>
> /David
>
>
> ------------------------------
> *From:* Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
> on behalf of Matthew Strugari <matthew.strugari at dal.ca>
> *Sent:* Tuesday, February 2, 2021 4:23 PM
> *To:* Cassandra Miller <cassandramiller at phas.ubc.ca>;
> gate-users at lists.opengatecollaboration.org <
> gate-users at lists.opengatecollaboration.org>
> *Subject:* Re: [Gate-users] Simulation crashes unexpectedly
>
>
> Hi Cassandra,
>
>
>
> Very strange. I also think it may be a memory issue, although maybe not
> related to simulation size in my case. My total simulation consumes ~4.6G
> of RAM out of 64G available. The issue has also never occurred during
> dosimetry-related experiments.
>
>
>
> I noticed that the issue began after I made some changes to my macro file
> in order to ensure that whole runs were distributed amongst the jobs. This
> required GATE to perform a number of internal alias comparisons and
> assignments. I have since cleaned up the alias and doif commands so
> hopefully that eliminates the issue since there were never any problems
> before adding those commands. Does your SPECT configuration utilize a lot
> of alias and doif commands as well?
>
>
>
> As another developer pointed out to me, the stderr printout means that a
> pointer to a physical volume pointed to an area of unused memory. I have
> always used the auto seed generator with the MersenneTwister option. If the
> issue persists, then I will manually set the seed to check if it crashes
> repeatedly. If it doesn’t crash with the same seed, then I am told it may
> be a problem with my computer.
>
>
>
> Thank you for your input!
>
> Matthew
>
>
>
>
>
> *From: *Cassandra Miller <cassandramiller at phas.ubc.ca>
> *Date: *Monday, February 1, 2021 at 19:35
> *To: *Matthew Strugari <matthew.strugari at dal.ca>
> *Subject: *Re: [Gate-users] Simulation crashes unexpectedly
>
> *CAUTION:* The Sender of this email is not from within Dalhousie.
>
> Hi Matthew,
>
> I don't have any insight into why this happens, but it happens to me ALL
> the time. The frequency it happens depends on the size of the simulation, I
> think it's a memory thing somehow. It's never happened to me using GATE
> actors for dosimetry, but it seems to exclusively happen when I'm doing
> SPECT imaging.
>
> The more jobs I split my simulation into, the less this happens. So
> sometimes in the past when I've ran simulations that are ridiculous in size
> or when I'm using specific sources (for example it happens way more with
> the fastY90 source than an ion source) I've split my sim into a stupid
> amount of jobs and then summed them up at the end. And wrote some scripts
> to automatically open and list the jobs that have crashed, go inside and
> change the engine seed number (I find if I change the engine seed it will
> not crash when I rerun it, but if I don't change the engine seed it will
> crash again), and re-run them.
>
> It sounds a bit ridiculous but.. I've opted to do that instead of figure
> out what causes the problem in the first place! So I'm sorry I can't help
> you with the root of the problem but there are ways around it at least.
>
> Best,
> Cassandra
>
> --
>
>
>
> Cassandra Miller
>
> PhD Student, Physics
>
> Quantitative Radiomolecular Imaging and Therapy Lab
>
> Department of Physics and Astronomy, University of British Columbia
>
> On 2021-02-01 2:36 p.m., Matthew Strugari wrote:
>
> Hi all,
>
>
>
> I am having difficulty determining why my simulation is crashing (see
> attached log file). I am using the task spooler to split my simulation into
> 12 jobs. Sometimes, one or more jobs will crash at the beginning of a run,
> but the run that GATE crashes on seems to be random (jobs have either 5 or
> 6 runs/projection images). Other times, all of the jobs will run to
> completion. After a job has crashed, I can reissue the command and the job
> will run to completion without error.
>
>
>
> I cannot figure out why the job(s) seemingly crash at random. Does anyone
> have any insight into the issue? Your assistance is greatly appreciated.
>
>
>
> Regards,
>
> Matthew
>
>
>
> --
>
> Matthew Strugari
>
> Biomedical Translational Imaging Centre - BIOTIC,
> 5890 University Ave,
> Halifax, NS, B3K 6R8
>
>
>
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