[Gate-users] Jobs killed "memory exceeded"?

Tue Sep 16 23:01:36 CEST 2014

Hi David,

Yes, I just checked a minute ago, and all three of the patches are
incorporated into the develop branch.
So I would modify my advice to this one:
Amy could try the latest development code, maybe it solves the memory
leak problem.
(This is actually better idea than just applying our patches, because
there is at least another one memory leak fix in the development
branch. (I did not check all the commits, so there may be more.))

In general, if somebody can create a short test GATE macro (the
shorter the better) for any bug, and he/she can share it, then it is
very useful for the actual code development.

Best,
  David

On Tue, Sep 16, 2014 at 9:12 PM, David Sarrut
<David.Sarrut at creatis.insa-lyon.fr> wrote:
> Hello,
>
> David : correct me if I am wrong, but those patches are already included in
> the develop branch of the git version, right ?
>
> thanks,
> David
>
> On Tue, Sep 16, 2014 at 1:43 PM, Dávid Völgyes <david.volgyes at gmail.com>
> wrote:
>>
>> Hi Amy,
>>
>> Hopefully, Sebastiens suggestion will help you, but if not, you can try
>> the followings:
>>
>> Gergely Patay and me sent some source code patches in June to the mailing
>> list, they could help.
>> The only drawback is that you have to compile GATE from source.
>>
>> Most of my fixes are related to memory leaks, but actually most of them
>> are ITK related, and I do not see any alfa/beta source specific
>> modification. Anyway, you can try these patches, it will not harm. If you do
>> so, please let us (the mailing list) know the result (helped or did not).
>>
>> Applying the patches is actually quite easy:
>>
>> First you have to download the patch files (see below), and uncompress
>> them with gunzip.
>>
>> After that you have to do everything exactly like the GATE install manual
>> says, except this part:
>>
>> - when you get a copy from the source:
>> git clone http://git.opengatecollaboration.org/git/opengate-public.git
>>
>> - then you have to enter to the GATE source directory:
>> cd opengate-public
>>
>> - and you have to apply the patches:
>> git apply  cppfix_dvolgyes.patch geant4-geometry.patch interfile.patch
>>
>> (the actual filenames can contain path-parts, like
>> ../patches/cppfix_dvolgyes.patch, it depends on your actual directory
>> layout.)
>>
>> After that you should follow the manual. (cmake, compile, install, etc.)
>>
>> As a last hope without actually debugging the code, you can try different
>> geant/root/gate/clhep versions,
>> maybe it comes from a recently introduced or recently fixed bug. Of
>> course, this takes a lot of time, and there is no guarantee for the success.
>>
>> (The original e-mail what contained the patches is quoted below my
>> signature.)
>>
>> Good luck!
>>
>> Cheers,
>>   David
>>
>> On Wed, Jun 18, 2014 at 10:54 AM, Patay Gergely <patay.gergely at mediso.hu>
>> wrote:
>> > Dear Gaters,
>> >
>> > here are a few patches against the upstream (ie. master branch) Gate
>> > source
>> > code. Since I am not a member of the collaboration, I cannot directly
>> > commit
>> > them into the git repository.
>> >
>> > The first patch was written by Dávid Völgyes (formerly at Mediso and at
>> > COMPET). These are C++ bugfixes (unchecked ranges, memory corruptions).
>> > [1]
>> >
>> > https://dl.dropboxusercontent.com/u/43097994/gate7/cppfix_dvolgyes.patch.gz
>> >
>> > The second patch contains Gate wrappers to all the missing Geant4 solid
>> > objects from
>> >
>> > http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch04.html
>> > .
>> > With this patch the following extra shapes will be available: cut tube,
>> > elliptical cone, generic trapezoid, hyperbolic tube, parallelepiped,
>> > paraboloid tube, tetrahedron, torus, twisted box, twisted trapezoid,
>> > generic
>> > twisted trapezoid and twisted tube segment.
>> > [2]
>> >
>> > https://dl.dropboxusercontent.com/u/43097994/gate7/geant4-geometry.patch.gz
>> >
>> > The third patch is a heavy modification of the Interfile reader. Besides
>> > some code cleaning and refactoring, it solves the following issues:
>> > - if the key 'name of data file' is present in the header file then it
>> > won't
>> > guess the name
>> > - the 'number of bytes per pixel' key (1,2,4,8...) is implemented
>> > - the 'data offset in bytes' key is implemented
>> > - the 'number format' key now accepts 'signed integer', 'unsigned
>> > integer',
>> > 'short float', 'long float' and (for convenience) 'float', as seen in
>> > the
>> > Interfile 3.3 standard.
>> > The interfile reader thus accepts signed or unsigned 8, 16, 32 or 64 bit
>> > integer as well as 32 (float) or 64 bit (double) floating point data
>> > from
>> > little or big endian binary file.
>> > [3]
>> > https://dl.dropboxusercontent.com/u/43097994/gate7/interfile.patch.gz
>> >
>> > cheers,
>> >  Gergely
>> >
>> > ---
>> > Gergely Patay
>> > physicist
>> > Mediso Medical Imaging Systems Ltd.
>> > Hungary
>>
>>
>>
>> On Tue, Sep 16, 2014 at 11:40 AM, JAN Sebastien <sebastien.jan at cea.fr>
>> wrote:
>>>
>>>
>>>
>>> Hi Amy,
>>>
>>> As explained by Marc, this is a memory leak…probably du to the fact that
>>> the energy of optical photons which are generated is out of the range
>>> defined in the xml files (material & surface). Try to correct that point and
>>> fell free to tell us if the problem is solved.
>>>
>>> Cheers
>>>
>>> Sebastien
>>>
>>>
>>>
>>>
>>>
>>> De : gate-users-bounces at lists.opengatecollaboration.org
>>> [mailto:gate-users-bounces at lists.opengatecollaboration.org] De la part de
>>> Marc Chamberland
>>> Envoyé : lundi 15 septembre 2014 16:06
>>> À : Amy Meldrum
>>> Cc : Gate Users
>>> Objet : Re: [Gate-users] Jobs killed "memory exceeded"?
>>>
>>>
>>>
>>> Hi Amy,
>>>
>>>
>>>
>>> Perhaps there is a memory leak? If there is, it's gonna be very annoying
>>> for you to troubleshoot if you have no C++ experience.
>>>
>>>
>>>
>>> I'd suggest you look at using Valgrind to detect memory leaks. You can
>>> find Valgrind here: http://valgrind.org
>>>
>>>
>>>
>>> The Quick Start page should help you run it. Feel free to post the output
>>> to the mailing list or send it to me and I'll have a quick look.
>>>
>>>
>>>
>>> Good luck!
>>>
>>> Marc
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> __________________________
>>>
>>>
>>>
>>> Marc Chamberland, MSc
>>>
>>> PhD candidate
>>> Department of Physics
>>> Carleton University
>>> Ottawa (ON)
>>>
>>>
>>>
>>> On Sep 14, 2014, at 8:55, Amy Meldrum <ameldru at g.clemson.edu> wrote:
>>>
>>>
>>>
>>> Gate users,
>>>
>>>
>>>
>>> I have been running simulations using optical photons that run to
>>> completion when I am using a beta source. However, when I change the source
>>> to an alpha source, suddenly all of my simulations only run for a few
>>> minutes before being killed. It seems like the memory usage skyrockets
>>> beyond some limit and get killed.
>>>
>>>
>>>
>>> Why would changing only the source do this? Is there something I can do
>>> to stop this from happening? The simulation runs fine for a few particles,
>>> but I am not sure why it would behave like this.
>>>
>>>
>>>
>>>
>>>
>>> Please help. Thank you,
>>>
>>>
>>>
>>> Amy
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>>
>>
>> _______________________________________________
>> 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 U 1044
> 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://www.creatis.insa-lyon.fr/~dsarrut
> _________________________________
>  "2 + 2 = 5,  for extremely large values of 2"
> _________________________________