[Gate-users] cylindrical volume crash
Eugene Gualtieri PhD
gualtier at mail.med.upenn.edu
Fri Aug 20 16:23:56 CEST 2010
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/
>
> _______________________________________________
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>
> /----------------------------------------------------------------------
> 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
>> ------------------------------------------------------------------------------------------------
>> ------------------------------------------------------------------------------------------------
>
>
> ------------------------------
>
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