[Gate-users] Fw: Problem with 'std::bad_alloc'

David Boersma david.boersma at physics.uu.se
Thu Jan 14 16:34:10 CET 2016


Hi Jared,

Thanks, that seems to work better indeed... :)

David

Den 14/01/2016 kl. 15:25, skrev STRYDHORST Jared:
> Using the emstandard_opt3 instead of QGSP physics list seems to work.
>
> Jared STRYDHORST
>
> Laboratoire Imagerie Moléculaire In Vivo (IMIV)
> UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
> CEA/I2BM/Service Hospitalier Frédéric Joliot
> 4, place du Général Leclerc
> 91401 ORSAY Cedex
>
> <mailto:karima.ait-aissa at cea.fr>
> http://i2bm.cea.fr/dsv/i2bm/shfj/imiv
> ------------------------------------------------------------------------
> *De :* gate-users-bounces at lists.opengatecollaboration.org
> [gate-users-bounces at lists.opengatecollaboration.org] de la part de
> Michal Knap [knap.michal at yahoo.com]
> *Envoyé :* jeudi 14 janvier 2016 13:35
> *À :* David Boersma; gate-users at lists.opengatecollaboration.org
> *Objet :* [Gate-users] Fw: Problem with 'std::bad_alloc'
>
> Hi All,
> I'm attaching my whole conversation with David and files below.
> Could you please help with solving this issue?
> It's a strange bug which causes huge consumption of RAM and gives me
>   this error message
>
> /       /terminate called after throwing an instance of 'std::bad_alloc'//
> /                            /  what(): std::bad_alloc/
> /
> /                             /Przerwane (core dumped)//
>
> My visualization doesn't even start but it is the smallest problem.
>
> I run benchmark simulation just to check if is everything all right with
> my Gate and it all works (benchmarkSPECT.mac with visualization works fine).
>
> I'm working on ubuntu 14.04 LTS / Geant4.9.6.p04 / Gate_v7.0/ ROOT 5.34.34.
> Onmachine with i5VPRO/2.4GHz/8GB/128 SSD.
>
> Can anybody help me with this issue?
> I'll be very thankful.
>
> Best Regards&Thanks
> Michał Knap
>
> 13:07 czwartek, 2016-1-14, David Boersma <david.boersma at physics.uu.se>
> napisał(a):
>
>
>
>
> Hi,
>
> All:
>
> Could other people please have a look at Michał's problem? I could run
> his macro (see his previous mail) and Gate indeed consumes excessive
> amounts of RAM, but it is not clear to me why that happens. See below
> for my observations. I have to work on other things now.
>
>
> Michał:
>
> Yes, I could run your macro. I disabled all the lines with "/vis" in
> them, ran the command "Gate ./minigamma1pointsourceoncollimator.mac" and
> then observed in a separate window with "htop" how things were going,
> resource-wise.
>
> I ran this on a machine with 16 GiB of RAM, Ubuntu 14.04, Geant
> 4.9.6.p04. It took about a minute to fill up all the RAM, and then it
> started to eat up the swap space. When it had eaten up 90% of the swap
> space I killed the program (from within htop; I was not able to kill
> Gate with ctrl-C).
>
> I think we can conclude that "something" in Gate is allocating too much
> memory. It could be a spectacular memory leak, or it could be some
> missconfigured component in your macro that causes excessive resource
> consumption. For the latter hypothesis I looked at your macro for
> suspicious things, but the most segmented thing I could find was the
> "projection" output, and replacing 128*128 by 4*4 did not help at all. I
> reduced the time slice from 1s to 0.001s and the time stop from 60s to
> 0.002s, but that did not seem to change anything either.
>
> Maybe there is some implicit/default setting that is wrong for your
> application. I am not an imaging expert (I use gate for radiotherapy),
> so maybe someone else has an idea.
>
> I ran it in "gdb" (the GNU debugger) and stopped the program by sending
> it a signal, while it was eating memory, and checked with "bt"
> (backtrace) in which function it was running at the moment I stopped it.
> I repeated this several times and got different backtraces every time,
> so this did not provide any useful hints for finding out which part of
> the code is responsible.
>
> This is as far as I could get, and the problem is not yet solved. I hope
> someone else on the list can take over to help you solve this. Maybe
> someone should run it with "valgrind", but that can be pretty time
> consuming, and maybe someone actually already knows, that would be much
> more efficient.
>
> Good luck,
> David B.
>
>
> Den 13/01/2016 kl. 20:26, skrev Michal Knap:
>  > Hi David,
>  > It would be really great if you could take a look on my mac file.
>  > Please see the attachment.
>  > I'm a little bit confused about this bug.
>  >
>  > I will try to try out your idea with much simplified version and will
>  > return with the results.
>  >
>  > Thanks&Regards
>  > Michał Knap
>  >
>  >
>  >
>  > 12:00 środa, 2016-1-13, David Boersma <david.boersma at physics.uu.se
> <mailto:david.boersma at physics.uu.se>>
>  > napisał(a):
>  >
>  >
>  > Hi Michał,
>  >
>  > On 2016-01-13 07:04, Michal Knap wrote:
>  >  > Hi David,
>  >  > I have only one version of Gate and Geant4 installed - Gate v7.0 and
>  >  > Geant4.9.6.p04.
>  >  >
>  >  > I successfully  run benchmark simulation - benchmarkSPECT, with or
>  >  > without visualization.
>  >  >
>  >  > So it's somthing with my code i think. What can i disable/enable
> to fix
>  >  > this bug?
>  >
>  > If there is indeed something wrong with your code then we can only help
>  > you by looking at your code.
>  >
>  > So, as I wrote in my previous mail, it would be nice if you could make a
>  > short and strongly simplified version of your macro which still crashes
>  > in the same way. Preferably it only uses input data from the examples
>  > and benchmarks. E.g. you define only a very crude geometry and a gamma
>  > source, and a number of primaries, no visualization. If that throws the
>  > same bad_alloc exception, then please send that to us, we can try to
>  > reproduce and tell you what's wrong. Of course it is possible that the
>  > problem disappears after you take out certain parts of the macro. If you
>  > can nail it down to one particular line or set of lines that makes the
>  > difference between crashing and not crashing, then quote those lines to
>  > us. That is less helpful the first option, but could still provide a
> hint.
>  >
>  > David B.
>  >
>  >
>  >  >
>  >  > Best regards
>  >  > Michał Knap
>  >  >
>  >  >
>  >  > 18:11 wtorek, 2016-1-12, David Boersma
> <david.boersma at physics.uu.se <mailto:david.boersma at physics.uu.se>
>  > <mailto:david.boersma at physics.uu.se
> <mailto:david.boersma at physics.uu.se>>>
>  >  > napisał(a):
>  >  >
>  >  >
>  >  > Hi Michał,
>  >  >
>  >  > Some more simple questions:
>  >  >
>  >  > * Can you run macros from the example directory successfully, or
> do some
>  >  > of them result in this same error?
>  >  >
>  >  >
>  >  > * Do you have multiple versions of Geant4 and/or Root installed?
> If yes,
>  >  > could you check with the following command:
>  >  >
>  >  > ldd $(which Gate)
>  >  >
>  >  > that your Gate executable gets indeed linked to the same versions
> as the
>  >  > ones you configured during installation of Gate? If the versions
> do not
>  >  > match: then fix your environment, or reinstall Gate (from scratch).
>  >  >
>  >  >
>  >  >
>  >  > If these simple questions do not help, then I think the next step
> is to
>  >  > make a minimalistic version of your macro that demonstrates the error
>  >  > you are seeing and post it here on the list, so that other people
> have a
>  >  > chance to reproduce this problem. Please also specify how you run the
>  >  > Gate command (with which options).
>  >  >
>  >  > HTH,
>  >  > David Boersma
>  >  >
>  >  > Den 12/01/2016 kl. 17:35, skrev Michal Knap:
>  >  >  > Hi David,
>  >  >  > I checked you idea but i use only 50-60% RAM memory.
>  >  >  > While i'm running simulation i do not use any other apps.
>  >  >  > Even browser is closed.
>  >  >  >
>  >  >  > I have intel i5 vPRO, 8GB RAM, 120 GB SSD
>  >  >  > Ubuntu 14.04 LTS, Geant4.9.6.p04,Gate7.0,Root 5.34.34
>  >  >  >
>  >  >  > Kind regards
>  >  >  >
>  >  >  >
>  >  >  > 17:01 wtorek, 2016-1-12, David Boersma
>  > <david.boersma at physics.uu.se <mailto:david.boersma at physics.uu.se>
> <mailto:david.boersma at physics.uu.se <mailto:david.boersma at physics.uu.se>>
>  >  > <mailto:david.boersma at physics.uu.se
> <mailto:david.boersma at physics.uu.se>
>  > <mailto:david.boersma at physics.uu.se
> <mailto:david.boersma at physics.uu.se>>>>
>  >  >  > napisał(a):
>  >  >  >
>  >  >  >
>  >  >  >
>  >  >  >
>  >  >  > Hi Michał,
>  >  >  >
>  >  >  > My first guess would be a memory problem. Could you check with some
>  >  >  > resource monitor ("top" or "htop" on linux, "Activity Monitory" on
>  >  >  > MacOSX) how much RAM is used on your machine, by which programs?
>  >  >  >
>  >  >  > It could be that other programs than GATE (e.g. a web browser) are
>  > using
>  >  >  > so much RAM that there is not enough available for your GATE
>  >  >  > application. Then this is easily solved by quitting those other
>  > programs.
>  >  >  >
>  >  >  > It could be that you configured GATE too optimistically, e.g.
> using a
>  >  >  > scoring volume with too many voxels. Then you should either use
> a more
>  >  >  > modest configuration, or run on a bigger machine.
>  >  >  >
>  >  >  > There are many other possible causes, but these are the easiest
>  > ones, I
>  >  >  > can think of. It would be good if you could tell us whether
> these are
>  >  >  > already ruled out.
>  >  >  >
>  >  >  > Also: when reporting problems and asking for help, it could be
> helpful
>  >  >  > if you would add some basic specs about the OS (+version) and the
>  >  >  > hardware (in particular how much RAM your have). Which version
> of GATE
>  >  >  > are you using, with which version of Geant4? How did you install
>  > it? Did
>  >  >  > you install it recently or long ago?
>  >  >  >
>  >  >  > HTH,
>  >  >  > David
>  >  >  >
>  >  >  > Den 12/01/2016 kl. 15:55, skrev Michal Knap:
>  >  >  >  > Hi All,
>  >  >  >  > As i'm trying to simulate a minigammacamera i'm getting this
> error
>  >  >  > message.
>  >  >  >  > I still do not know how to fix this.
>  >  >  >  > Can anybody know what is wrong?
>  >  >  >  > //
>  >  >  >  > /[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final
>  >  > stop at
>  >  >  >  > 150 s./
>  >  >  >  > /terminate called after throwing an instance of
> 'std::bad_alloc'/
>  >  >  >  > /  what():  std::bad_alloc/
>  >  >  >  > /Przerwane (core dumped)/
>  >  >  >  > /
>  >  >  >  > /
>  >  >  >  > I'll be very thankful for any help.
>  >  >  >  >
>  >  >  >  > Thanks in advance
>  >  >  >  >
>  >  >  >  > Kind regards
>  >  >  >  > Michał Knap
>  >  >  >
>  >  >  >  >
>  >  >  >  >
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