[gate-users] voxelized phantoms Gate 1.2

[Mutanga Theodore]

Hello there

I already solved most of my problems, it was actually the digitizer module
that was not loading , I had mistakenly commented the part that was
supposed to call the digitizer macro. Now the jobs is running and I can
see the root file is filling up slowly.
Theo other messages I mentioned in the last post was because of the
verbosity level of the source manager.

Thanks for the suggestions.

> 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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