[Gate-users] cylindrical volume crash

Eugene Gualtieri PhD gualtier at mail.med.upenn.edu
Fri Aug 20 19:27:50 CEST 2010 

Hi Rony,

Thanks for your reply.  

Once again I should have pasted more of the script, sorry.

I already had the world geometry set quite a bit larger than the scanner geometry:

/gate/world/geometry/setXLength 400. cm
/gate/world/geometry/setYLength 400. cm
/gate/world/geometry/setZLength 400. cm


-gene


On Aug 20, 2010, at 1:08 PM, Rony A. wrote:

> Dear Gene,
> 
> The problem might be that, while using this example the way it is written, without defining your 'world' geometry, may result that a part of your geometry is outside the world, if by default the predefined world shape is 50x50x50 cm3. (since Rmax of your CPET is 60cm).
> 
> I would suggest to start by:
> 
> /gate/world/geometry/setXLength 200. cm
> /gate/world/geometry/setYLength 200. cm
> /gate/world/geometry/setZLength 200. cm
> 
> followed by the CPET example commands.
> 
> Sorry I can't access Gate at the moment on my personal computer to check it, but I think it's worth a try. 
> 
> Please tell me if it works.
> 
> Regards,
> Rony.
> 
> On Fri, Aug 20, 2010 at 4:23 PM, Eugene Gualtieri PhD <gualtier at mail.med.upenn.edu> wrote:
> Hi Bryan,
> 
> Thanks for your reply!
> 
> I'm afraid that's not the problem though.  (Looks like my prior email had a cut/paste error, sorry)
> 
> What I should have said was that using the CPET example verbatim from the 5.0 GATE Users Guide causes a crash:
> 
> # BASE = CPET SYSTEM
> /gate/world/daughters/name CPET
> /gate/world/daughters/insert cylinder
> /gate/CPET/setMaterial Air
> /gate/CPET/geometry/setRmax 60 cm
> /gate/CPET/geometry/setRmin 0.0 cm
> /gate/CPET/geometry/setHeight 35.0 cm
> /gate/CPET/vis/forceWireframe
> 
> # FIRST LEVEL = CRYSTAL
> /gate/CPET/daughters/name crystal
> /gate/CPET/daughters/insert cylinder
> /gate/crystal/geometry/setRmax 47.5 cm
> /gate/crystal/geometry/setRmin 45.0 cm
> /gate/crystal/geometry/setHeight 25.6 cm
> /gate/crystal/geometry/setPhiStart 0 deg
> /gate/crystal/geometry/setDeltaPhi 60 deg
> 
> # REPEAT THE CURVE SECTOR INTO THE WHOLE RING
> /gate/crystal/repeaters/insert ring
> /gate/crystal/ring/setRepeatNumber 6
> 
> # CRYSTAL VOLUME IS MADE OF LSO
> /gate/crystal/setMaterial LSO
> /gate/crystal/vis/setColor green
> 
> /gate/systems/CPET/crystal/attach crystal
> 
> #Sensitive detector.    Set the crystals as sensitive detectors (see section 5.2.1, p.82).
> /gate/crystal/attachCrystalSD
> 
> Thanks!
> 
> -gene
> 
> 
> On Aug 20, 2010, at 6:00 AM, gate-users-request at lists.opengatecollaboration.org wrote:
> 
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> > Today's Topics:
> >
> >   1. Re: cylindrical volume crash (Bryan McIntosh)
> >   2. Re: "/gate/random/setEngineSeed auto" always generates   the
> >      same results (Uwe Pietrzyk)
> >   3. Re: "/gate/random/setEngineSeed auto" always generates the
> >      same results (Franck P. Vidal)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 19 Aug 2010 07:27:56 -0500
> > From: Bryan McIntosh <mcintoshster at gmail.com>
> > Subject: Re: [Gate-users] cylindrical volume crash
> > To: gate-users at lists.opengatecollaboration.org
> > Message-ID:
> >       <AANLkTinsxmNKb4P10RWyq63vN7xVFY1JCro0CPzWZZO_ at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Gene,
> >
> > It looks like your simulation is crashing because you forgot to define
> > the size of the crystal before you attached it.  Set a height/radius
> > for it first, then any repeaters needed before you try to attach it to
> > a system.
> >
> > Hope this solves your problem!
> >
> > -Bryan
> >
> >> Message: 1
> >> Date: Wed, 18 Aug 2010 14:01:48 -0400
> >> From: Eugene Gualtieri PhD <gualtier at mail.med.upenn.edu>
> >> Subject: [Gate-users] cylindrical crystal volume crash
> >> To: gate-users at lists.opengatecollaboration.org
> >> Message-ID: <21BF8364-C9A6-4968-A6A8-F194CD352AD7 at mail.med.upenn.edu>
> >> Content-Type: text/plain; charset=us-ascii
> >>
> >> All:
> >>
> >> I am encountering a segmentation fault when specifying cylindrical crystal volumes, as in the CPET scanner example.
> >> The seg fault occurs right after the "/gate/systems/CPET/crystal/attach crystal" line (see below). ?Commenting it out eliminates the crash.
> >>
> >> I am running ?GATE version name: gate_v5.0.0 ?(1-May-2009)
> >>
> >> Thanks.
> >>
> >> Gene
> >>
> >>
> >> # BASE = CPET SYSTEM
> >> /gate/world/daughters/name CPET
> >> /gate/world/daughters/insert cylinder
> >> /gate/CPET/setMaterial Air
> >> /gate/CPET/geometry/setRmax 60 cm
> >> /gate/CPET/geometry/setRmin 0 cm
> >> /gate/CPET/geometry/setHeight 35 cm
> >> /gate/CPET/vis/forceWireframe
> >>
> >> # FISRT LEVEL = CRYSTAL
> >> /gate/CPET/daughters/name crystal
> >> /gate/CPET/daughters/insert cylinder
> >>
> >> /gate/systems/CPET/crystal/attach crystal
> >> /gate/crystal/attachCrystalSD
> >>
> >>
> >> ===================
> >> /gate/systems/CPET/crystal/attach crystal
> >>
> >> ?*** Break *** segmentation violation
> >> Attaching to program: /proc/28902/exe, process 28902
> >> [Thread debugging using libthread_db enabled]
> >> 0x00007f4edd7dbb0e in waitpid () from /lib/libc.so.6
> >> error detected on stdin
> >> A debugging session is active.
> >>
> >> ? ? ? ?Inferior 1 [process 28902] will be detached.
> >>
> >> Quit anyway? (y or n) [answered Y; input not from terminal]
> >> Detaching from program: /proc/28902/exe, process 28902
> >> *** glibc detected *** Gate: free(): invalid pointer: 0x00000000020fb268 ***
> >> =========
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 19 Aug 2010 16:16:34 +0200
> > From: Uwe Pietrzyk <u.pietrzyk at fz-juelich.de>
> > Subject: Re: [Gate-users] "/gate/random/setEngineSeed auto" always
> >       generates       the same results
> > To: Franck P.Vidal <franck.p.vidal at gmail.com>
> > Cc: "gate-users at lists.opengatecollaboration.org"
> >       <gate-users at lists.opengatecollaboration.org>
> > Message-ID: <F15C0FA3-5575-4E8A-BFD2-6867F9DA0F88 at fz-juelich.de>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> > Hi Franck,
> >
> > I could reproduce your results, but also found a kind of temporary
> > solution:
> > It seems to be related to the "imageCT" option, since when I
> > disable this option by issuing : " /gate/output/imageCT/disable"
> > and only use the "/gate/random/setEngineSeed auto"
> > the files are different!
> > I am sure, that you can get the same information of imageCT by
> > writing the data out of a root-programm, although I haven't done so yet
> > by myself.
> >
> > Hope this helps.
> >
> > Kind regards,
> >
> > Uwe
> > -----
> > On 19.08.2010, at 00:47, Franck P. Vidal wrote:
> >
> > Hi there,
> >
> > I set the random number generator as follows:
> >   /gate/random/setEngineName MersenneTwister
> >   /gate/random/setEngineSeed auto
> >   /gate/random/verbose 1
> >
> > Every time I run my simulation, the output is always identical (e.g.
> > when I enable the ASCII output in "example_CT/fast"
> > benchmarkFastCTHits.dat, or the raw data benchmarkFastCT_000.dat),
> > whereas the initial seeds are different.
> >
> > Even with   /gate/random/setEngineSeed   567489   I get the same output.
> >
> > Is there any reason for that?
> > I was expecting the results to be different.
> >
> > Best Regards,
> >
> > Franck
> >
> > --
> > Dr Franck P. Vidal
> > Postdoctoral Research Fellow
> >
> > Department of Radiation Oncology
> > University of California, San Diego
> > Moores Cancer Center, Rm 1410
> > 3855 Health Sciences Dr. #0843
> > La Jolla, CA 92093-0843
> > Tel: (858)822-7499
> > Fax: (858)822-6078
> > Homepage: http://pagesperso-orange.fr/f-p.v/
> >
> > _______________________________________________
> > 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
> >
> > /----------------------------------------------------------------------
> > Prof. Dr. Uwe Pietrzyk
> > Diplom-Physiker
> > Institut f?r Neurowissenschaften und Medizin / INM-1
> > Forschungszentrum J?lich GmbH
> > 52425 J?lich
> > Tel: +49-2461-61 4763
> > Fax: +49-2461-61 2820 + 8229
> > Mobil: +49-162-103-4871
> > eMail: U.Pietrzyk at fz-juelich.de<mailto:U.Pietrzyk at fz-juelich.de>
> > http://www.fz-juelich.de/inm<http://www.fz-juelich.de/inb/inb-3/>
> > &
> > Bergische Universit?t Wuppertal
> > Fachbereich C - Physik / D.08.01
> > Gau?str. 20
> > 42097 Wuppertal
> > Tel: +49-(0)202-439-3523
> > Fax: +49-(0)202-439-2811
> > eMail: Uwe.Pietrzyk at physik.uni-wuppertal.de<mailto:Uwe.Pietrzyk at physik.uni-wuppertal.de>
> > http://www.medizinphysik.uni-wuppertal.de<http://www.medizinphysik.uni-wuppertal.de/>
> > ----------------------------------------------------------------------/
> >
> >
> >
> >
> >
> >
> >
> >
> > ------------------------------------------------------------------------------------------------
> > ------------------------------------------------------------------------------------------------
> > Forschungszentrum Juelich GmbH
> > 52425 Juelich
> > Sitz der Gesellschaft: Juelich
> > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> > Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
> > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> > Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> > Prof. Dr. Sebastian M. Schmidt
> > ------------------------------------------------------------------------------------------------
> > ------------------------------------------------------------------------------------------------
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 19 Aug 2010 10:13:38 -0700
> > From: "Franck P. Vidal" <franck.p.vidal at gmail.com>
> > Subject: Re: [Gate-users] "/gate/random/setEngineSeed auto" always
> >       generates the same results
> > To: Uwe Pietrzyk <u.pietrzyk at fz-juelich.de>
> > Cc: "gate-users at lists.opengatecollaboration.org"
> >       <gate-users at lists.opengatecollaboration.org>
> > Message-ID: <4C6D6642.4020708 at gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Hi Uwe,
> >
> > I disabled the imageCT output, and yes, it works...
> > Thanks for the suggestion!
> >
> > Best regards,
> >
> > Franck
> >
> > --
> > Dr Franck P. Vidal
> > Postdoctoral Research Fellow
> >
> > Department of Radiation Oncology
> > University of California, San Diego
> > Moores Cancer Center, Rm 1410
> > 3855 Health Sciences Dr. #0843
> > La Jolla, CA 92093-0843
> > Tel: (858)822-7499
> > Fax: (858)822-6078
> > Homepage: http://pagesperso-orange.fr/f-p.v/
> >
> >
> > On 08/19/2010 07:16 AM, Uwe Pietrzyk wrote:
> >>
> >> Hi Franck,
> >>
> >> I could reproduce your results, but also found a kind of temporary
> >> solution:
> >> It seems to be related to the "imageCT" option, since when I
> >> disable this option by issuing : " /gate/output/imageCT/disable"
> >> and only use the "/gate/random/setEngineSeed auto"
> >> the files are different!
> >> I am sure, that you can get the same information of imageCT by
> >> writing the data out of a root-programm, although I haven't done so yet
> >> by myself.
> >>
> >> Hope this helps.
> >>
> >> Kind regards,
> >>
> >> Uwe
> >> -----
> >> On 19.08.2010, at 00:47, Franck P. Vidal wrote:
> >>
> >>> Hi there,
> >>>
> >>> I set the random number generator as follows:
> >>>   /gate/random/setEngineName MersenneTwister
> >>>   /gate/random/setEngineSeed auto
> >>>   /gate/random/verbose 1
> >>>
> >>> Every time I run my simulation, the output is always identical (e.g.
> >>> when I enable the ASCII output in "example_CT/fast"
> >>> benchmarkFastCTHits.dat, or the raw data benchmarkFastCT_000.dat),
> >>> whereas the initial seeds are different.
> >>>
> >>> Even with   /gate/random/setEngineSeed   567489   I get the same output.
> >>>
> >>> Is there any reason for that?
> >>> I was expecting the results to be different.
> >>>
> >>> Best Regards,
> >>>
> >>> Franck
> >>>
> >>> --
> >>> Dr Franck P. Vidal
> >>> Postdoctoral Research Fellow
> >>>
> >>> Department of Radiation Oncology
> >>> University of California, San Diego
> >>> Moores Cancer Center, Rm 1410
> >>> 3855 Health Sciences Dr. #0843
> >>> La Jolla, CA 92093-0843
> >>> Tel: (858)822-7499
> >>> Fax: (858)822-6078
> >>> Homepage: http://pagesperso-orange.fr/f-p.v/
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >> /----------------------------------------------------------------------
> >> Prof. Dr. Uwe Pietrzyk
> >> Diplom-Physiker
> >> Institut f?r Neurowissenschaften und Medizin / INM-1
> >> Forschungszentrum J?lich GmbH
> >> 52425 J?lich
> >> Tel: +49-2461-61 4763
> >> Fax: +49-2461-61 2820 + 8229
> >> Mobil: +49-162-103-4871
> >> eMail: U.Pietrzyk at fz-juelich.de <mailto:U.Pietrzyk at fz-juelich.de>
> >> http://www.fz-juelich.de/inm <http://www.fz-juelich.de/inb/inb-3/>
> >> &
> >> Bergische Universit?t Wuppertal
> >> Fachbereich C - Physik / D.08.01
> >> Gau?str. 20
> >> 42097 Wuppertal
> >> Tel: +49-(0)202-439-3523
> >> Fax: +49-(0)202-439-2811
> >> eMail: Uwe.Pietrzyk at physik.uni-wuppertal.de
> >> <mailto:Uwe.Pietrzyk at physik.uni-wuppertal.de>
> >> http://www.medizinphysik.uni-wuppertal.de
> >> <http://www.medizinphysik.uni-wuppertal.de/>
> >> ----------------------------------------------------------------------/
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> ------------------------------------------------------------------------------------------------
> >> ------------------------------------------------------------------------------------------------
> >> Forschungszentrum Juelich GmbH
> >> 52425 Juelich
> >> Sitz der Gesellschaft: Juelich
> >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> >> Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
> >> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> >> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> >> Prof. Dr. Sebastian M. Schmidt
> >> ------------------------------------------------------------------------------------------------
> >> ------------------------------------------------------------------------------------------------
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >
> > End of Gate-users Digest, Vol 51, Issue 15
> > ******************************************
> 
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