[Gate-users] !! Gate v6.0.0 on Mac OS X >>still not OK

Chen, Yu Yu.Chen at umassmed.edu
Wed Mar 3 21:46:43 CET 2010


We at Walter Reed Army Medical Center tested GATE V6 beta version at Mac OS X 10.5.8 last December and had the problem to include the physics processes. Please see below a message sent to Seb by one researcher in our group on Dec 18, 2009 for details. 
 
Look forward to seeing this problem fixed soon.
 
Yu Chen, PhD
Remote Proton Radiation Therapy
Walter Reed Army Medical Center
Bldg 2, Rm 1H46A
6900 Georgia Avenue, NW
Washington, DC 20307
Phone: (202) 782-1881
Fax: (202) 782-0305
E-mail: yu.chen at amedd.army.mil
 
-----Original Message-----
From: Kramer, Kevin M Mr CTR USA MEDCOM WRAMC
Sent: Friday, December 18, 2009 3:09 PM
To: Seb
Subject: RE: GATE V6 beta version test (UNCLASSIFIED)

Classification:  UNCLASSIFIED
Caveats: NONE

Hello Sebastien,

I am a research scientist at Walter Reed Army Medical Center and have been
testing the GateV6 sources here.  I have run into a problem that you may be
interested in or maybe can help me with.

I am running the code on a Mac OS X Server 10.5.8.  I'm using Geant4.9.2.p02
and CLHEP 2.0.4.5 and ROOT version 5.20.

The code compiles successfully without error. I am trying to run the
benchmark codes provided, but get the following warnings when I run the
macros :

<!> *** WARNING *** <!>  Unknown process: PhotoElectric
<!> *** WARNING *** <!>  Unknown process: Compton
<!> *** WARNING *** <!>  Unknown process: GammaConversion
<!> *** WARNING *** <!>  Unknown process: LowEnergyRayleighScattering
<!> *** WARNING *** <!>  Unknown process: ElectronIonisation
<!> *** WARNING *** <!>  Unknown process: Bremsstrahlung
<!> *** WARNING *** <!>  Unknown process: PositronAnnihilationStd
<!> *** WARNING *** <!>  Unknown process: MultipleScattering
<!> *** WARNING *** <!>  Unknown process: MultipleScattering

List of Enabled processes:


List of initialized processes:

The code runs, but produces junk output (the physics is not loading
correctly I'm guessing).  I modified just to print out the output of the
addprocess line in the macro and I find its trying to load the process with
the  "Default" particle.  I don't know if that information helps or not. 

Let me know if you are the right person to send this to, or if I am doing
something wrong.

Thanks,
Kevin


Kevin Kramer
Henry M. Jackson Foundation for the Advancement of Military Medicine
Walter Reed Army Medical Center
Building 2 1H46A
Washington, DC 20307
(202)782-1883




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Today's Topics:

   1. Re: !! Gate v6.0.0 on Mac OS X >>still not OK (Didier Benoit)


----------------------------------------------------------------------

Message: 1
Date: Wed, 03 Mar 2010 00:28:33 +0100
From: Didier Benoit <benoit at cppm.in2p3.fr>
Subject: Re: [Gate-users] !! Gate v6.0.0 on Mac OS X >>still not OK
To: Uwe Pietrzyk <u.pietrzyk at fz-juelich.de>
Cc: gate-users at lists.opengatecollaboration.org
Message-ID: <4B8D9F21.9080304 at cppm.in2p3.fr>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Uwe,

Yes it's the "normal" bug :), the processes are not loaded in GATE6 on
Mac Os X.

Kind regards,
Didier

Le 03/03/2010 00:25, Uwe Pietrzyk a ?crit :
>
> Hi,
>
> I briefly tested the benchPET. I could start GATE, but there is nothing
> written to the root-file after 20 min. Also, the visualisation does
> not work
> and crashes the X11-environment ...
>
> So I will wait until bugs are solved. Let me know, when I can continue
> testing Gate6 on Mac Os X ...
>
> Kind regards,
>
> Uwe
> -----
> On 03.03.2010, at 00:01, Pietrzyk, Uwe wrote:
>
>>
>> Hi Marc, hi Didier,
>>
>> omitting the lmf-library was the key! On 64-bit-systems, I found the lmf
>> not working anymore and you are right to disable it, in case you are not
>> interested in.
>> According to Didier, I will not start any production on my Mac until the
>> bugs are fixed.
>>
>> Many thanks and kind regards,
>>
>> Uwe
>>
>> -----
>> On 02.03.2010, at 20:55, Didier Benoit wrote:
>>
>>> Hi Uwe and Marc,
>>>
>>> Yes, the problem is in the physical processes. It' a bug in the
>>> "GateVProcess" and "GatePhysicsList" classes. I hope I could fix
>>> this bug the next week, and surely there will be a new patch
>>> (gate_v6.0.1).
>>>
>>> Kind Regards,
>>> Didier
>>>
>>> Le 02/03/2010 20:41, Marc Chamberland a ?crit :
>>>> Hi Uwe,
>>>>
>>>> I had the same problem as you, but disabling the LMF libraries (which I don't expect to use for now) solved it.
>>>>
>>>> However, Didier pointed out that there are problems with certain processes on Mac OS X. Indeed, when I tried running the benchmark for PET, Gate didn't recognize any of the physical processes. I'll wait for the coming fix in the meantime.
>>>>
>>>> Cheers!
>>>> Marc
>>>>
>>>>
>>>> Le 2010-03-02 ? 14:26, Uwe Pietrzyk a ?crit :
>>>>
>>>>   
>>>>> Hi Didier, hi Marc,
>>>>>
>>>>> it didn't work in my case. I recompiled Geant4 and Gate and starting
>>>>> Gate without any .mac file runs into the idle prompt, which looks fine, I thought.
>>>>> But starting the the benchmark gives me:
>>>>>
>>>>> medmac37.ime.kfa-juelich.de  <http://medmac37.ime.kfa-juelich.de/>  75 /Applications/gate_v6.0.0/benchmarks/benchPET -->  Gate benchPET.mac
>>>>> [G4]
>>>>> [G4] *************************************************************
>>>>> [G4]  Geant4 version Name: geant4-09-02-patch-03    (29-January-2010)
>>>>> [G4]                       Copyright : Geant4 Collaboration
>>>>> [G4]                       Reference : NIM A 506 (2003), 250-303
>>>>> [G4]                             WWW :http://cern.ch/geant4
>>>>> [G4] *************************************************************
>>>>> [G4]
>>>>> [Core-0] Initialization of geometry
>>>>> [Core-0] Initialization of physics
>>>>> [Core-0] Initialization of actors
>>>>> [Core-0]
>>>>> [Core-0] **********************************************************************
>>>>> [Core-0]  GATE version name: gate_v6
>>>>> [Core-0]                     Copyright : OpenGATE Collaboration
>>>>> [Core-0]                     Reference : Phys. Med. Biol. 49 (2004) 4543-4561
>>>>> [Core-0]                     WWW :http://www.opengatecollaboration.org/
>>>>> [Core-0] **********************************************************************
>>>>> [Core-0]
>>>>> [Core-0] Starting macro benchPET.mac
>>>>> dyld: lazy symbol binding failed: Symbol not found: _fillEHforGATE
>>>>>    Referenced from: /Applications/gate_v6.0.0/tmp/Darwin-g++/Gate/libGate.dylib
>>>>>    Expected in: flat namespace
>>>>>
>>>>> dyld: Symbol not found: _fillEHforGATE
>>>>>    Referenced from: /Applications/gate_v6.0.0/tmp/Darwin-g++/Gate/libGate.dylib
>>>>>    Expected in: flat namespace
>>>>>
>>>>> Trace/BPT trap
>>>>>
>>>>> In rebuilding Geant4 I have created shared and static libraries at the same time.
>>>>> This was an option, but could this cause a problem?
>>>>> Would it be useful to go back to the static solution Mac OS X again?
>>>>>
>>>>> Marc, did you change anything else?
>>>>>
>>>>> Kind regards,
>>>>>
>>>>> Uwe
>>>>>
>>>>> On 02.03.2010, at 17:45, Marc Chamberland wrote:
>>>>>
>>>>>     
>>>>>> Thank you very much for your help, Didier. Compiling Geant4 with shared libraries worked to fix my problem. If anything else comes up, I'll let the mailing list know.
>>>>>>
>>>>>> Thanks again!
>>>>>> Marc
>>>>>>
>>>>>>
>>>>>> Le 2010-03-02 ? 03:57, Didier BENOIT a ?crit :
>>>>>>
>>>>>>       
>>>>>>> Hi Marc,
>>>>>>>
>>>>>>> Actually GATE 6 has some problems on Mac OS (concerning the processes), We are tracking the problems encountered by the Mac users and should be able to provide a solution soon.
>>>>>>>
>>>>>>> But I can launch GATE:
>>>>>>> [Mar mar 02 09:30:32 dbenoit at Ixtl ~]$ Gate
>>>>>>> [G4]
>>>>>>> [G4] *************************************************************
>>>>>>> [G4]  Geant4 version Name: geant4-09-02-patch-03    (29-January-2010)
>>>>>>> [G4]                       Copyright : Geant4 Collaboration
>>>>>>> [G4]                       Reference : NIM A 506 (2003), 250-303
>>>>>>> [G4]                             WWW :http://cern.ch/geant4
>>>>>>> [G4] *************************************************************
>>>>>>> [G4]
>>>>>>> [Core-0] Initialization of geometry
>>>>>>> [Core-0] Initialization of physics
>>>>>>> [Core-0] Initialization of actors
>>>>>>> [Core-0]
>>>>>>> [Core-0] **********************************************************************
>>>>>>> [Core-0]  GATE version name: gate_v6
>>>>>>> [Core-0]                     Copyright : OpenGATE Collaboration
>>>>>>> [Core-0]                     Reference : Phys. Med. Biol. 49 (2004) 4543-4561
>>>>>>> [Core-0]                     WWW :http://www.opengatecollaboration.org/
>>>>>>> [Core-0] **********************************************************************
>>>>>>> [Core-0]
>>>>>>> Idle>
>>>>>>>
>>>>>>> Could you check if your GEANT is installed with the shared libraries?
>>>>>>> To check this, source your file env_gate.sh and check this line:
>>>>>>>
>>>>>>> .......
>>>>>>> On this machine the G4LIB_BUILD_SHARED=1
>>>>>>> .......
>>>>>>>
>>>>>>> If you are "On this machine the G4LIB_BUILD_SHARED=0" you have to reinstall GEANT4 :(.
>>>>>>>
>>>>>>> There the line to build the shared libraries in GEANT4:
>>>>>>> Do you want to build 'shared' (.so) libraries?[n] y
>>>>>>> You selected to build 'shared' (.so) libraries.
>>>>>>>
>>>>>>> Hope this help,
>>>>>>> Kind regards,
>>>>>>> Didier
>>>>>>>
>>>>>>> Le 2 mars 2010 ? 02:31, Marc Chamberland a ?crit :
>>>>>>>
>>>>>>>         
>>>>>>>> Thanks for the reply, Uwe. Unfortunately, I haven't found any solution yet since my C++ skills are quite limited. For those having the same problem, it seems related to the PostStepDoIt( const G4Track&, const G4Step&) function, from the G4VEmProcess class in Geant4. This function is referred to from only 3 places in Gate:
>>>>>>>>
>>>>>>>> 1) In GateFictitiousFastSimulationModel.cc on line 240.
>>>>>>>>
>>>>>>>> 2&  3) In the GateGenericWrapperProcess and GateTotalDiscreteProcess classes. They each define a PostStepDoIt function, but it looks like they're also using the G4VEmProcess version of the function in their definition.
>>>>>>>>
>>>>>>>> I'm not sure if this information is useful to solve the issue or not, but it can't hurt to put it out there.
>>>>>>>>
>>>>>>>> Cheers!
>>>>>>>> Marc
>>>>>>>>
>>>>>>>> Le 2010-03-01 ? 03:52, Uwe Pietrzyk a ?crit :
>>>>>>>>
>>>>>>>>           
>>>>>>>>> Hi Marc,
>>>>>>>>>
>>>>>>>>> I am facing exactly the same problem, except that my setting is slightly different:
>>>>>>>>> Mac OS X 10.6.2, Geant4.9.2.p02, CLHEP 2.0.3.2, gcc 4.2.1, root 5.24 and like
>>>>>>>>> in your case Gate_v5.0.0_p01 is working fine.
>>>>>>>>>
>>>>>>>>> Since I use the c-shell and could not find the env_gate.csh in Gate 6, I took the one from
>>>>>>>>> Gate 5 and modified it slightly.
>>>>>>>>> I also compared the file GateCommon.gmk which obviously is the former variables.gmk
>>>>>>>>> and found that LDFLAGS have been modified in GateCOmmon.gmk. In Mac OS X, there
>>>>>>>>> is no /usr/X11R6/lib64, only /usr/X11R6/lib, hence I adjusted this too, but it did not
>>>>>>>>> solve the problem we both experienced.
>>>>>>>>> Something fundamental must have been changed during the transition to Gate 6.
>>>>>>>>>
>>>>>>>>> Kind regards,
>>>>>>>>>
>>>>>>>>> Uwe
>>>>>>>>>
>>>>>>>>> On 28.02.2010, at 21:42, Marc Chamberland wrote:
>>>>>>>>>
>>>>>>>>>             
>>>>>>>>>> Hi Gate Users!
>>>>>>>>>>
>>>>>>>>>> I've compiled Gate v6.0.0. Everything seemed fine during compilation, but when I try to launch Gate, I get the following error:
>>>>>>>>>>
>>>>>>>>>> Compiling Gate.cc ...
>>>>>>>>>> Using granular libraries ...
>>>>>>>>>> Linking Gate
>>>>>>>>>> ... Done!
>>>>>>>>>> [/Applications/gate_v6.0.0] Marc$ Gate
>>>>>>>>>> dyld: Symbol not found: __ZN12G4VEmProcess12PostStepDoItERK7G4TrackRK6G4Step
>>>>>>>>>> Referenced from: /Applications/gate_v6.0.0/tmp/Darwin-g++/Gate/libGate.dylib
>>>>>>>>>> Expected in: flat namespace
>>>>>>>>>> in /Applications/gate_v6.0.0/tmp/Darwin-g++/Gate/libGate.dylib
>>>>>>>>>> Trace/BPT trap
>>>>>>>>>> [/Applications/gate_v6.0.0] Marc$
>>>>>>>>>>
>>>>>>>>>> I'm on Mac OS X 10.6.2, with Geant4 9.2.p03, clhep 2.0.4.2, and gcc version 4.2.1 (Apple Inc. build 5646). For the record, I recently (two weeks ago) installed Gate v5.0.0 and didn't encounter this problem.
>>>>>>>>>>
>>>>>>>>>> Can anyone help me with this? Thank you in advance!
>>>>>>>>>>
>>>>>>>>>> Marc
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Gate-users mailing list
>>>>>>>>>> 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
>>>>>>>>> http://www.fz-juelich.de/inm
>>>>>>>>> &
>>>>>>>>> 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
>>>>>>>>> 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
>>>>>>>>> Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
>>>>>>>>> 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
>>>>>>>>           
>>>>>>> ----------------------------------------------------------------
>>>>>>> Didier BENOIT, Ing?nieur GATE
>>>>>>> Imagerie et Mod?lisation en Neurobiologie et Canc?rologie (IMNC)
>>>>>>> IMNC - UMR 8165 CNRS - Universit? Paris 7 - Universit? Paris 11
>>>>>>> Campus d'Orsay
>>>>>>> B?timent 440
>>>>>>> 91406 ORSAY Cedex
>>>>>>>
>>>>>>> T?l: (33) 1 69 15 36 46
>>>>>>> E-mail:benoit at imnc.in2p3.fr
>>>>>>>         benoit at cppm.in2p3.fr
>>>>>>> http://www.imnc.in2p3.fr <http://www.imnc.in2p3.fr/> 
>>>>>>> ----------------------------------------------------------------
>>>>>>>
>>>>>>>         
>>>>>> _______________________________________________
>>>>>> Gate-users mailing list
>>>>>> 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
>>>>> http://www.fz-juelich.de/inm
>>>>> &
>>>>> 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
>>>>> http://www.medizinphysik.uni-wuppertal.de <http://www.medizinphysik.uni-wuppertal.de/> 
>>>>> ----------------------------------------------------------------------/
>>>>>
>>>>>     
>>>> _______________________________________________
>>>> Gate-users mailing list
>>>> Gate-users at lists.opengatecollaboration.org
>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>   
>>>
>>>
>>> --
>>>
>>> */----------------------------------------------------------------/*
>>>
>>> */Didier BENOIT, Ing?nieur GATE/*
>>>
>>> */Imagerie et Mod?lisation en Neurobiologie et Canc?rologie (IMNC)/*
>>>
>>> */IMNC ? UMR 8165 CNRS ? Universit? Paris 7 ? Universit? Paris 11/*
>>>
>>> */Campus d?Orsay/*
>>>
>>> */B?timent 440/*
>>>
>>> */91406 ORSAY Cedex/*
>>>
>>> */ /*
>>>
>>> */T?l : (33) 1 69 15 36 46/*
>>>
>>> */E-mail : benoit at imnc.in2p3.fr <mailto:benoit at imnc.in2p3.fr>/*
>>>
>>> */http://www.imnc.in2p3.fr <http://www.imnc.in2p3.fr/>  <http://www.imnc.in2p3.fr/>/*
>>>
>>> */----------------------------------------------------------------/*
>>>
>>
>> /----------------------------------------------------------------------
>> 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
>> &
>> 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/> 
>> <http://www.medizinphysik.uni-wuppertal.de/>
>> ----------------------------------------------------------------------/
>>
>
> /----------------------------------------------------------------------
> 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
> &
> 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/> 
> <http://www.medizinphysik.uni-wuppertal.de/>
> ----------------------------------------------------------------------/
>


--

*/----------------------------------------------------------------/*

*/Didier BENOIT, Ing?nieur GATE/*

*/Imagerie et Mod?lisation en Neurobiologie et Canc?rologie (IMNC)/*

*/IMNC ? UMR 8165 CNRS ? Universit? Paris 7 ? Universit? Paris 11/*

*/Campus d?Orsay/*

*/B?timent 440/*

*/91406 ORSAY Cedex/*

*/ /*

*/T?l : (33) 1 69 15 36 46/*

*/E-mail : benoit at imnc.in2p3.fr <mailto:benoit at imnc.in2p3.fr>/*

*/http://www.imnc.in2p3.fr/*

*/----------------------------------------------------------------/*



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