[Gate-users] problem with random number seed?
David Sarrut
David.Sarrut at creatis.insa-lyon.fr
Tue Feb 2 11:00:38 CET 2016
Hello,
just a short comment: GATE is not validated at all with MT Geant4, and
should not be used with Geant4 MT.
Modifying Gate to use Geant4 MT capabilities would require lot of work and
is not currently planned.
David
On Mon, Feb 1, 2016 at 5:29 PM, David Boersma <david.boersma at physics.uu.se>
wrote:
> Hi,
>
> Den 01/02/2016 kl. 17:08, skrev Andrej:
>
>> A quick and dirty fix is to set the randomSeed to some run related
>> number. I know that in geant people would sometimes start each event
>> with a seed equal to that event number. Here you only have to do it
>> run-wise.
>>
>
> Unfortunately when we try that we still get identical outputs for
> successive runs.
>
> I think that the problem is not in how Gate obtains a seed (from
> /dev/random with "auto" or reading a literal user-supplied value from the
> macro), but rather in how Gate communicates that seed to (a multithreaded
> version of) the geant4 library.
>
> David
>
>
>> Cheers
>>
>> Andrej
>>
>> surabhi balagopal nair je 2/1/2016 ob 4:40 PM napisal:
>>
>>> Hello,
>>>
>>> Can anyone tell me whether the Virtual Gate is built on GEANT4
>>> multithread ON or OFF?
>>>
>>> Thank you,
>>> SN
>>>
>>> On 1 February 2016 at 10:14, David Boersma
>>> <david.boersma at physics.uu.se <mailto:david.boersma at physics.uu.se>>
>>> wrote:
>>>
>>> Hi,
>>>
>>> It looks like Thomas Deschler was right: random number seeding in
>>> Gate (current develop version, but I suspect the conclusions also
>>> hold for release 7.1) only works correctly if the Geant4 10.1
>>> libraries were compiled with multithreading OFF. By "correctly" we
>>> mean: with "auto" seeding you get a different seed every time you
>>> run it, and therefore statistically independent outputs. If you
>>> use a geant4 installation built with multithreading=ON, then
>>> successive Gate runs will give identical outputs.
>>>
>>> We verified this (on Linux and on MacOSX) by compiling Geant4 with
>>> and without multithreading, and then building Gate with it. We ran
>>> Hediye's minimal RT macro (shoot electrons on a target foil, and
>>> collect a phasespace of the particles after it, stored in a ROOT
>>> output file). We ran the macro twice (renaming the output
>>> directory in between). "Ekine" histograms of the two runs were
>>> numerically identical when we ran *with* multithreading and they
>>> were clearly different *without* multithreading.
>>>
>>> Short term action item: it would be good to document this clearly
>>> in the README file and/or the 7.1 installation guide on the wiki.
>>>
>>> Medium/long term action item: fix Gate to work correctly with
>>> multithreaded geant4.
>>>
>>> I have more comments, but they are more technical, will submit
>>> them as "issues" on GitHub.
>>>
>>> HTH,
>>> David B.
>>>
>>>
>>> Den 01/02/2016 kl. 11:18, skrev hediye acun:
>>>
>>> Hello Loic,
>>>
>>> We tried your recommendations with David Boersma. First we
>>> run main
>>> macro file for 20 particles and stored output in PhS_new.root
>>> file. We
>>> got particle's properties(location and energy) in root with
>>> Scan command
>>> and then we closed root to make sure root will not remember
>>> the first
>>> output file due to the same tree's name. We run main macro
>>> second time
>>> with same particle number(20) to get second output file which
>>> called
>>> PhS_try.root. In root with scan we obtained particle's
>>> properties again
>>> for second run. After that we compared two text files which
>>> include
>>> particle's location and energies and there was no difference
>>> between them.
>>>
>>> David Boersma run same macro file in his computer which has
>>> Geant4
>>> compiled with multithread OFF, and he obtained different
>>> results for
>>> same number of primaries. My Geant4 compiled with multithread
>>> ON. We
>>> are going to try to compile on my computer with multitherad
>>> OFF and on
>>> David's computer multithread ON to investigate whether it
>>> really depends
>>> on the multithreading.
>>>
>>> Best regards.
>>>
>>> Hediye acun
>>>
>>> PS. It looks like the mailing list not working today. David
>>> didn't
>>> receive your reply and we didn't see on the archive either.
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> *From:* Grevillot Loic <loic.grevillot at medaustron.at
>>> <mailto:loic.grevillot at medaustron.at>>
>>> *To:* hediye acun <acunhediye at yahoo.com
>>> <mailto:acunhediye at yahoo.com>>;
>>> "gate-users at lists.opengatecollaboration.org
>>> <mailto:gate-users at lists.opengatecollaboration.org>"
>>> <gate-users at lists.opengatecollaboration.org
>>> <mailto:gate-users at lists.opengatecollaboration.org>>
>>>
>>> *Sent:* Monday, February 1, 2016 9:20 AM
>>> *Subject:* RE: [Gate-users] problem with random number seed?
>>>
>>> Hello,
>>> In my experience the command"/gate/random/setEngineSeed
>>> auto"works.
>>> In your example you are looking at histograms, but to verify
>>> that issue
>>> I was thinking about something different:
>>> -If the seed did not change as you suspect, the physical
>>> properties from
>>> every single particle stored in your Phase Space one after the
>>> other
>>> shall be exactly the same (position, direction, energy, etc.)
>>> for 2
>>> simulations.
>>> -Could you check that on a particle basis for 10 or 20 particles?
>>> You could even try a very simple example where you could
>>> randomly sample
>>> 10 particles and look if they are the same for 2 simulations.
>>> Let us know!
>>> Thanks
>>>
>>> Image:Uncle_Sam_pointing_finger_small.jpgImage:We-Need-You1-324x500.jpgImage:superdupont-we-need-you.jpgImage:gsam_want_gnu_small.jpg
>>> *//**/GATE is a /**/research community/**/, /**/ please
>>> contribute!/*//
>>> *You just started? You found some errors in the examples and the
>>> documentation?*
>>> § You can correct the documentation
>>> <http://wiki.opengatecollaboration.org/index.php/Main_Page> on
>>> the wiki
>>> web site
>>> § You can share your experience on the user mailing-list
>>> <http://www.opengatecollaboration.org/mailinglist>
>>> **
>>> *You have a few months of experience or more?*
>>> § You can correct or even propose new examples
>>> <http://www.opengatecollaboration.org/Examples>
>>> § You can propose a new gate actor, it is as easy as a plug-in!
>>> <http://wiki.opengatecollaboration.org/index.php/GateActor>
>>> *You are now an official Gate addict and you need more?*
>>> § You can participate in Gate C++ source code development:
>>> debugging,
>>> propose new classes, etc.
>>> ðFor new developments, use git
>>> <http://www.opengatecollaboration.org/Git> and contact the
>>> gate-devel-mailing-list
>>> <http://www.opengatecollaboration.org/mailinglist> to be guided.
>>> *//**/Thanks for your contribution, the OpenGate collaboration!/*
>>> *From:*gate-users-bounces at lists.opengatecollaboration.org
>>> <mailto:gate-users-bounces at lists.opengatecollaboration.org>
>>> [mailto:gate-users-bounces at lists.opengatecollaboration.org
>>> <mailto:gate-users-bounces at lists.opengatecollaboration.org>]
>>> *On Behalf
>>> Of *hediye acun
>>> *Sent:* Friday, January 29, 2016 3:46 PM
>>> *To:* gate-users at lists.opengatecollaboration.org
>>> <mailto:gate-users at lists.opengatecollaboration.org>
>>>
>>> *Subject:* [Gate-users] problem with random number seed?
>>> Hello All,
>>> I have Gate "develop" version and at the same time
>>> geant4.10.1.0 and
>>> root_v5.34.32 on the GPU. My operating system is Linux Mint 17.2
>>> .
>>> I am triying to simulate a linac head to get Phase Space of
>>> photons.
>>> Just for an example I run Gate for a basic geometry which
>>> include only
>>> electron beam, target filter and Phase space plane inside a linac
>>> geometry. When I run Gate two or more times for same "number of
>>> primaries" I got the exactly the same Phase Space distributions
>>> (histogram of Ekine completely identical). But I am using
>>> "/gate/random/setEngineSeed auto" command and according to the
>>> documentation that should give me the different seed every
>>> time when I
>>> run it. I would expect some random differences between PhS's from
>>> different runs.
>>> Does anyone have any idea about this issue? Thank you in advance.
>>> Hediye Acun
>>> *Disclaimer:*
>>> Please notice our E-Mail Disclaimer
>>> http://www.medaustron.at/email-disclaimer/
>>>
>>>
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> <mailto: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
>>
>> _______________________________________________
> 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 U1206
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/20160202/9d8e714c/attachment-0001.html>
More information about the Gate-users
mailing list