[gate-users] voxelized phantoms Gate 1.2

[ziad bitar]

Hi Theodore,
I mean by swapping the fact that the Job overflow the
RAM and thus computation will be done partially on the
hard disc which may lead the system to be decelerated
and frequently scratched.
I am running Gate 2,2 with Geant4.7.0 version and i
have no problems.
To control if there is any swapping just type the
command "top" in the shell where you've launched your
simulation and you can see the evolution of the usage
of the memory (using more than 90% of the memory is
bad sign).

Unfortunately, i don't have anymore the example i've
used for the validation.
Good luck
Ziad
--- Mutanga Theodore <muathe02 at student.umu.se> wrote:

> Hi Ziad,
> 
> Thanks for the suggestion but Im running the same
> version of Geant4 6.2p02
> which is recommended for Gate 2.1 and root 4.04.
> Whad did you mean by swapping ? I am running GATE on
> the cluster and it is
> version 2.1 thats installed. I had tried Gate 2,2 
> on another cluster and
> I couldn't run Gate with voxelized phantom and
> sources. I got the errors I
> had mentioned on a previous post about bad
> allocation. Do you have some
> macros that work let me try them out  and see..
> 
> 
> cheers
> 
> Theo
> 
> 
> > Good Morning,
> > I suggest to verify if there is any swapping while
> the
> > Job is running.
> > I've had this problem few times ago and it was a
> > problem of non compatibility between the Geant4
> > version and the Gate Version.
> >
> > I propose to migrate from gate_v2.1.0 to
> gate_v2.2.0
> > which is compatible with geant4.7.0.p01.
> >
> > Greetings
> > Ziad
> > --- Mutanga Theodore <muathe02 at student.umu.se>
> wrote:
> >
> >> Greetings all,
> >>
> >> I have been puzzled by the behaviour of gate for
> the
> >> past couple of days
> >> now and I would like to have some help from
> anyone
> >> with simillar
> >> experiences or someone who has an idea.
> >>
> >> I am using Gate 2.1 with all configurations as
> shown
> >> on the site.
> >>
> >> I have created my phantom from CT image slices
> using
> >> PMOD and Xmedcon for
> >> conversion into interfile. The image data is
> >> unsigned integer and I have
> >> verified this by dumping the pixels to screen.
> >>
> >> Now I run a complete benchmark test with PET
> >> benchmark and it goes without
> >> any problems in about 6 hours and the results are
> >> ok.
> >>
> >> I then modify the same benchmark macro with wth
> my
> >> own camera, and phantom
> >> modules. I use also a modified version of the
> >> Voxelized sources and
> >> Voxelized phantom macros to test my simulation.
> >>
> >> What is puzzling is that there are no errors in
> the
> >> output but the
> >> simulation seems to hand just after the part
> where
> >> range cuts are
> >> calculated ....the last  line is the line with
> >> -------default region of
> >> the world------
> >>
> >> I constantly check the root file size during the
> >> simulation but it doesn't
> >> change in size. I have used a total or 15 MBq for
> a
> >> total of 2550760
> >> voxels.  and I am just testing for a 5 seconds
> run.
> >> (start - stop = 5s)
> >>
> >>
> >> Is anyone running voxelized sources and phantoms
> >> with this version ? Could
> >> I please have some macros and sample interfile
> >> phantoms to test and
> >> compare with mine ?
> >>
> >> I don't have any idea why the simulation is not
> >> working as everything is
> >> ok and no error messages are presented.
> >>
> >> Thanks for your help.
> >>
> >> Greetings
> >>
> >>
> >>
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> >>
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> >>
> >
> >
> >
> >
> >
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