[Gate-users] Gate-users Digest, Vol 107, Issue 32
abdallah smida
a_smida at yahoo.fr
Tue Apr 14 19:09:56 CEST 2015
Please don't send me your mails in future
Le Mardi 14 avril 2015 17h19, "gate-users-request at lists.opengatecollaboration.org" <gate-users-request at lists.opengatecollaboration.org> a écrit :
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Today's Topics:
1. Re: ion source timestamp bug, Gate 7.1 (Gergely Patay)
2. Re: Gate 7.1 build broken after updating to Geant4.10.01.p01
(Alex Vergara Gil)
3. Re: Gate 7.1 build broken after updating to Geant4.10.01.p01
(Marc Verderi)
4. Geant4 and Eclipse (imen elhamrouni)
5. Re: Root not working in VGate 3.0 (Mathieu DUPONT)
----------------------------------------------------------------------
Message: 1
Date: Tue, 14 Apr 2015 15:13:32 +0200
From: Gergely Patay <gergely.patay at mediso.com>
To: Gate User <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] ion source timestamp bug, Gate 7.1
Message-ID: <552D127C.7040800 at mediso.com>
Content-Type: text/plain; charset="utf-8"; format=flowed
Dear Gaters,
to answer my own question: the problem is indeed deep inside Geant4, and as
usual, originally this is "not a bug, but a feature".
In GateVSource.cc:268 we (try to) force life time of the source particle to zero:
// Force life time to 0, time is managed by GATE not G4
GetParticleDefinition()->SetPDGLifeTime(0);
However, from v10.0+ when Geant4 reads back the life time of a general ion
source, it does *not* retrieve the previously set value, but an (otherwise
physically correct) value from an external data file
(G4ENSDFSTATE1.0/ENSDFSTATE.dat) :
G4ParticleDefinition.icc:45
inline
G4double G4ParticleDefinition::GetPDGLifeTime() const
{
if(IsGeneralIon())
{ return GetIonLifeTime(); }
else
{ return thePDGLifeTime; }
}
Unfortunately, the underlying isGeneralIon variable is not directly accessible
from outside (i.e. from Gate).
A minimal workaround might be as follows:
1) change visibility of isGeneralIon from protected to public:
geant4/particles/management/include/G4ParticleDefinition.hh:402
- protected:
+ public:
G4bool isGeneralIon;
(this might be modified *without* recompiling Geant4)
2) add the following line to gate/source/physics/src/GateVSource.cc:269
GetParticleDefinition()->SetPDGLifeTime(0);
+ GetParticleDefinition()->isGeneralIon=false;
3) recompile Gate with the modified header file.
Since this modification affects Geant4 code too, I cannot provide a simple patch
file yet.
best regards,
Gergely
--
Gergely Patay
Mediso Ltd.
On 2015-04-01 13:38, Gergely Patay wrote:
> Dear Gaters,
>
> I installed the latest version of Gate from git. Everything went fine
> (benchmarks etc), until I tried to use the 'generic ion' source for a PET
> simulation.
>
> The timestamps of the hits (and consequently, of the singles and coincidences)
> are weird. They should be distributed uniformly in the [0,1] s interval (as seen
> on the ion_timestamp_gate7.0.png figure), but in 7.1 they are distributed
> exponentially over a much-much larger time interval with an exponent which
> equals to the decay rate of the ion, in this case Na-22.
>
> The macro files were identical, and the corresponding software versions were
> - Gate7.0, Geant4.9.6.p03, root5.34.18
> - Gate7.1, Geant4.10.01, root5.34.26
>
> This bug is actually the very same to that was reported on March 31, 2011 for
> Gate 6.0.1
> (http://lists.opengatecollaboration.org/mailman/private/gate-users/2011-March/004895.html)
> which somehow disappeared from 7.0 but re-emerged in 7.1.
>
> The bug does not affect the backtoback or e+ sources, and energy spectra are fine.
> It might be buried somewhere deep in Geant4.
>
> Do you have any idea what went wrong?
>
> thanks,
> Gergely
>
> --
> Gergely Patay
> Mediso Ltd.
>
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
------------------------------
Message: 2
Date: Tue, 14 Apr 2015 09:16:01 -0400
From: Alex Vergara Gil <alexvergaragil at gmail.com>
To: REUZE SYLVAIN <SYLVAIN.REUZE at gustaveroussy.fr>
Cc: Gate Users <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Gate 7.1 build broken after updating to
Geant4.10.01.p01
Message-ID:
<CAMF2x=nDWVfRCzt5sn0RuhkwBpEme594sZpB70+Z_N5pbjtO4Q at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Indeed! In the G4 page there is no link to the source code of 10.1
version without the patch01.
This is dangerous for Gate, shall it be created a mirror image of the
current working G4 source code in the
http://www.opengatecollaboration.org page??? I think this would be a
temporary solution at least for now.
Regards
Alex
2015-04-14 9:06 GMT-04:00, REUZE SYLVAIN <SYLVAIN.REUZE at gustaveroussy.fr>:
> Hello,
>
>
>
> I have the same compilation errors with Geant4 10.01 p01. I'd like to
> install Gate 7.1 in order to solve another problem, but I can't find the
> link to download Geant4 10.01, without the patch.
>
> Could you help me ?
>
>
>
> Best regards,
>
> Sylvain Reuz?
> Stagiaire physicien
> D?partement de Radioth?rapie
> Service de physique m?dicale
>
> T?l. : 01 42 11 54 06
> www.gustaveroussy.fr<http://www.gustaveroussy.fr>
> [cid:image001.gif at 01D076C4.8D1D9C60]
>
>
>
>
>
>
>
> -----Message d'origine-----
> De : gate-users-bounces at lists.opengatecollaboration.org
> [mailto:gate-users-bounces at lists.opengatecollaboration.org] De la part de
> Alex Vergara Gil
> Envoy? : lundi 13 avril 2015 13:12
> ? : Marc Chamberland
> Cc : Gate Users
> Objet : Re: [Gate-users] Gate 7.1 build broken after updating to
> Geant4.10.01.p01
>
>
>
> For what it's worth, I can reproduce the compilation errors, too.
>
> There might be a compatibility issue with the
>
> G4SPSRandomGenerator.hh:156:7:
>
> error: field of type 'G4Cache<G4SPSRandomGenerator::a_check>' has
>
> private copy constructor
>
> class G4SPSRandomGenerator {
>
>
>
> I'm compiling with:
>
>
>
> GCC version 4.8
>
>
>
> Alex
>
>
>
> 2015-04-10 11:53 GMT-04:00, Marc Chamberland
>
> <MarcChamberland at cmail.carleton.ca>:
>
>> For what it's worth, I can reproduce the compilation errors, too. I'm
>
>> compiling with:
>
>>
>
>> Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
>
>>
>
>>
>
>> Marc
>
>>
>
>>
>
>>
>
>> __________________________
>
>>
>
>> Marc Chamberland, MSc
>
>> PhD candidate
>
>> Department of Physics
>
>> Carleton University
>
>> Ottawa (ON)
>
>>
>
>>> On Apr 9, 2015, at 17:17, Mojca Miklavec
>>> <mojca.miklavec.lists at gmail.com>
>
>>> wrote:
>
>>>
>
>>> Hi,
>
>>>
>
>>> Today I updated Geant4 from version 4.10.01 to 4.10.01.p01 and Gate no
>
>>> longer compiles for me. Below is the first error (followed by many
>
>>> others). I was surprised because Geant4 developers aren't really known
>
>>> for breaking backward compatibility with patch releases.
>
>>>
>
>>> I'm using clang 3.4 which is not fully C++11 compatible (at least not
>
>>> without switching to a different stdlib) in case that this was the
>
>>> reason for the failure.
>
>>>
>
>>> I will try to investigate where the problem could be, but I wanted to
>
>>> report an issue. Maybe others will be able to reproduce it and
>
>>> diagnose it faster than I can. (There is a chance that it's not
>
>>> related to the code in Gate and that Geant4 is to blame.)
>
>>>
>
>>> Mojca
>
>>>
>
>>>
>
>>>
>
>>> [ 87%] Building CXX object
>
>>> CMakeFiles/Gate.dir/source/physics/src/GateVSourceMessenger.cc.o
>
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
>
>>> -DG4INTY_USE_QT -DG4UI_USE -DG4UI_USE_QT -DG4UI_USE_TCSH -DG4VERBOSE
>
>>> -DG4VIS_USE -DG4VIS_USE_OPENGL -DG4VIS_USE_OPENGLQT
>
>>> -DG4_STORE_TRAJECTORY -pipe -Os -arch x86_64 -stdlib=libstdc++ -W
>
>>> -Wall -pedantic -Wno-non-virtual-dtor -Wno-long-long -Wwrite-strings
>
>>> -Wpointer-arith -Woverloaded-virtual -Wno-variadic-macros -Wshadow
>
>>> -pipe -Qunused-arguments -std=c++98 -pipe -Os -arch x86_64
>
>>> -stdlib=libstdc++ -Wno-shadow -DNDEBUG -DNDEBUG -arch x86_64
>
>>> -mmacosx-version-min=10.7 -F//System/Library/Frameworks
>
>>> -I/opt/local/libexec/root5/include/root -I/path/to/build -isystem
>
>>> /opt/local/include/Geant4/Geant4.10.1/Geant4 -isystem
>
>>> /opt/local/include -isystem /opt/local/include/QtCore -isystem
>
>>> /opt/local/include/QtGui -isystem /opt/local/include/QtOpenGL
>
>>> -I/path/to/Gate-a20d5f0/source/arf/include
>
>>> -I/path/to/Gate-a20d5f0/source/geometry/include
>
>>> -I/path/to/Gate-a20d5f0/source/physics/include
>
>>> -I/path/to/Gate-a20d5f0/source/digits_hits/include
>
>>> -I/path/to/Gate-a20d5f0/source/general/include
>
>>> -I/path/to/Gate-a20d5f0/source/externals/clhep/include
>
>>> -I/path/to/Gate-a20d5f0/source/externals/itk-mhd
>
>>> -I/path/to/Gate-a20d5f0/source/externals/itk-mhd/itkzlib
>
>>> -I/path/to/Gate-a20d5f0/source/externals/itk-mhd/MetaIO
>
>>> -I/path/to/build/itk-mhd -o
>
>>> CMakeFiles/Gate.dir/source/physics/src/GateVSourceMessenger.cc.o -c
>
>>> /path/to/Gate-a20d5f0/source/physics/src/GateVSourceMessenger.cc
>
>>> In file included from
>
>>> /path/to/Gate-a20d5f0/source/physics/src/GateVSource.cc:16:
>
>>> In file included from
>
>>> /path/to/Gate-a20d5f0/source/physics/include/GateBackToBack.hh:14:
>
>>> In file included from
>
>>> /path/to/Gate-a20d5f0/source/physics/include/GateVSource.hh:16:
>
>>> In file included from
>
>>> /opt/local/include/Geant4/Geant4.10.1/Geant4/G4SingleParticleSource.hh:124:
>
>>> In file included from
>
>>> /opt/local/include/Geant4/Geant4.10.1/Geant4/G4SPSPosDistribution.hh:141:
>
>>> /opt/local/include/Geant4/Geant4.10.1/Geant4/G4SPSRandomGenerator.hh:156:7:
>
>>> error: field of type 'G4Cache<G4SPSRandomGenerator::a_check>' has
>
>>> private copy constructor
>
>>> class G4SPSRandomGenerator {
>
>>> ^
>
>>> _______________________________________________
>
>>> 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
>
------------------------------
Message: 3
Date: Tue, 14 Apr 2015 15:21:17 +0200
From: Marc Verderi <verderi at in2p3.fr>
To: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Gate 7.1 build broken after updating to
Geant4.10.01.p01
Message-ID: <552D144D.5050808 at in2p3.fr>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear all,
Andrea Dotti <adotti at slac.stanford.edu>, from Geant4, has been informed
of the problem. Could involved Gate developers contact him for providing
a solution ?
Cheers,
Marc
On 04/14/2015 03:16 PM, Alex Vergara Gil wrote:
> Indeed! In the G4 page there is no link to the source code of 10.1
> version without the patch01.
>
> This is dangerous for Gate, shall it be created a mirror image of the
> current working G4 source code in the
> http://www.opengatecollaboration.org page??? I think this would be a
> temporary solution at least for now.
>
> Regards
> Alex
>
>
> 2015-04-14 9:06 GMT-04:00, REUZE SYLVAIN <SYLVAIN.REUZE at gustaveroussy.fr>:
>> Hello,
>>
>>
>>
>> I have the same compilation errors with Geant4 10.01 p01. I'd like to
>> install Gate 7.1 in order to solve another problem, but I can't find the
>> link to download Geant4 10.01, without the patch.
>>
>> Could you help me ?
>>
>>
>>
>> Best regards,
>>
>> Sylvain Reuz?
>> Stagiaire physicien
>> D?partement de Radioth?rapie
>> Service de physique m?dicale
>>
>> T?l. : 01 42 11 54 06
>> www.gustaveroussy.fr<http://www.gustaveroussy.fr>
>> [cid:image001.gif at 01D076C4.8D1D9C60]
>>
>>
>>
>>
>>
>>
>>
>> -----Message d'origine-----
>> De : gate-users-bounces at lists.opengatecollaboration.org
>> [mailto:gate-users-bounces at lists.opengatecollaboration.org] De la part de
>> Alex Vergara Gil
>> Envoy? : lundi 13 avril 2015 13:12
>> ? : Marc Chamberland
>> Cc : Gate Users
>> Objet : Re: [Gate-users] Gate 7.1 build broken after updating to
>> Geant4.10.01.p01
>>
>>
>>
>> For what it's worth, I can reproduce the compilation errors, too.
>>
>> There might be a compatibility issue with the
>>
>> G4SPSRandomGenerator.hh:156:7:
>>
>> error: field of type 'G4Cache<G4SPSRandomGenerator::a_check>' has
>>
>> private copy constructor
>>
>> class G4SPSRandomGenerator {
>>
>>
>>
>> I'm compiling with:
>>
>>
>>
>> GCC version 4.8
>>
>>
>>
>> Alex
>>
>>
>>
>> 2015-04-10 11:53 GMT-04:00, Marc Chamberland
>>
>> <MarcChamberland at cmail.carleton.ca>:
>>
>>> For what it's worth, I can reproduce the compilation errors, too. I'm
>>> compiling with:
>>> Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
>>> Marc
>>> __________________________
>>> Marc Chamberland, MSc
>>> PhD candidate
>>> Department of Physics
>>> Carleton University
>>> Ottawa (ON)
>>>> On Apr 9, 2015, at 17:17, Mojca Miklavec
>>>> <mojca.miklavec.lists at gmail.com>
>>>> wrote:
>>>> Hi,
>>>> Today I updated Geant4 from version 4.10.01 to 4.10.01.p01 and Gate no
>>>> longer compiles for me. Below is the first error (followed by many
>>>> others). I was surprised because Geant4 developers aren't really known
>>>> for breaking backward compatibility with patch releases.
>>>> I'm using clang 3.4 which is not fully C++11 compatible (at least not
>>>> without switching to a different stdlib) in case that this was the
>>>> reason for the failure.
>>>> I will try to investigate where the problem could be, but I wanted to
>>>> report an issue. Maybe others will be able to reproduce it and
>>>> diagnose it faster than I can. (There is a chance that it's not
>>>> related to the code in Gate and that Geant4 is to blame.)
>>>> Mojca
>>>> [ 87%] Building CXX object
>>>> CMakeFiles/Gate.dir/source/physics/src/GateVSourceMessenger.cc.o
>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
>>>> -DG4INTY_USE_QT -DG4UI_USE -DG4UI_USE_QT -DG4UI_USE_TCSH -DG4VERBOSE
>>>> -DG4VIS_USE -DG4VIS_USE_OPENGL -DG4VIS_USE_OPENGLQT
>>>> -DG4_STORE_TRAJECTORY -pipe -Os -arch x86_64 -stdlib=libstdc++ -W
>>>> -Wall -pedantic -Wno-non-virtual-dtor -Wno-long-long -Wwrite-strings
>>>> -Wpointer-arith -Woverloaded-virtual -Wno-variadic-macros -Wshadow
>>>> -pipe -Qunused-arguments -std=c++98 -pipe -Os -arch x86_64
>>>> -stdlib=libstdc++ -Wno-shadow -DNDEBUG -DNDEBUG -arch x86_64
>>>> -mmacosx-version-min=10.7 -F//System/Library/Frameworks
>>>> -I/opt/local/libexec/root5/include/root -I/path/to/build -isystem
>>>> /opt/local/include/Geant4/Geant4.10.1/Geant4 -isystem
>>>> /opt/local/include -isystem /opt/local/include/QtCore -isystem
>>>> /opt/local/include/QtGui -isystem /opt/local/include/QtOpenGL
>>>> -I/path/to/Gate-a20d5f0/source/arf/include
>>>> -I/path/to/Gate-a20d5f0/source/geometry/include
>>>> -I/path/to/Gate-a20d5f0/source/physics/include
>>>> -I/path/to/Gate-a20d5f0/source/digits_hits/include
>>>> -I/path/to/Gate-a20d5f0/source/general/include
>>>> -I/path/to/Gate-a20d5f0/source/externals/clhep/include
>>>> -I/path/to/Gate-a20d5f0/source/externals/itk-mhd
>>>> -I/path/to/Gate-a20d5f0/source/externals/itk-mhd/itkzlib
>>>> -I/path/to/Gate-a20d5f0/source/externals/itk-mhd/MetaIO
>>>> -I/path/to/build/itk-mhd -o
>>>> CMakeFiles/Gate.dir/source/physics/src/GateVSourceMessenger.cc.o -c
>>>> /path/to/Gate-a20d5f0/source/physics/src/GateVSourceMessenger.cc
>>>> In file included from
>>>> /path/to/Gate-a20d5f0/source/physics/src/GateVSource.cc:16:
>>>> In file included from
>>>> /path/to/Gate-a20d5f0/source/physics/include/GateBackToBack.hh:14:
>>>> In file included from
>>>> /path/to/Gate-a20d5f0/source/physics/include/GateVSource.hh:16:
>>>> In file included from
>>>> /opt/local/include/Geant4/Geant4.10.1/Geant4/G4SingleParticleSource.hh:124:
>>>> In file included from
>>>> /opt/local/include/Geant4/Geant4.10.1/Geant4/G4SPSPosDistribution.hh:141:
>>>> /opt/local/include/Geant4/Geant4.10.1/Geant4/G4SPSRandomGenerator.hh:156:7:
>>>> error: field of type 'G4Cache<G4SPSRandomGenerator::a_check>' has
>>>> private copy constructor
>>>> class G4SPSRandomGenerator {
>>>> ^
>>>> _______________________________________________
>>>> 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
>>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
------------------------------
Message: 4
Date: Tue, 14 Apr 2015 16:47:15 +0200
From: imen elhamrouni <imenelhamrouni at gmail.com>
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] Geant4 and Eclipse
Message-ID:
<CAMaL-We2FxJYTeK_jYhpLu3F9cw9Qm5HQA_sGfohhLs-yscG5g at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello all,
Is There any way to run an example of Geant4 ,B1 for example, from a new
project in eclipse , which are the libraries i should add to this
project? Is there any specific configuration for eclipse?What should i do
?..
Thanks!
Imen
?
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------------------------------
Message: 5
Date: Tue, 14 Apr 2015 18:19:09 +0200 (CEST)
From: Mathieu DUPONT <mdupont at cppm.in2p3.fr>
To: BERGAMASCHI Antoine <antoine.bergamaschi at synchrotron-soleil.fr>
Cc: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Root not working in VGate 3.0
Message-ID:
<1799207786.5910617.1429028349637.JavaMail.zimbra at cppm.in2p3.fr>
Content-Type: text/plain; charset=utf-8
Hi Antoine,
you are right. It's not working.
For the libjpeg missing, simply do :
sudo apt-get install libjpeg62
And after that, you will miss some ?libtiff stuff?.
To fix this, I did
sudo apt-get install libtiff4
sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.4 /usr/lib/libtiff.so.3
And it's working now (at least, the Draw() command in root). It's not a clean solution, but I hope it will help you.
Mathieu Dupont
----- Original Message -----
From: "BERGAMASCHI Antoine" <antoine.bergamaschi at synchrotron-soleil.fr>
To: gate-users at lists.opengatecollaboration.org
Sent: Tuesday, April 14, 2015 10:05:51 AM
Subject: [Gate-users] Root not working in VGate 3.0
Hi all,
Everything is in the title, i am using the Gate V delivered as the version 3.0 and the root programme crash when using the "draw()" method due to the lack or a corrupted "libjpeg.so.62" and the fail to load libASImage.so ( which is present in the directory ).
I did not change a single bit of configuration on the VM.
Is a working version of the very usefull vGate disponible anywhere to download ?
Best regards,
Antoine Bergamaschi
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
------------------------------
_______________________________________________
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http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
End of Gate-users Digest, Vol 107, Issue 32
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