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

Tue Sep 16 21:12:32 CEST 2014

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"
_________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140916/503a2c74/attachment-0001.html>