[Gate-users] Trouble installing GATE
Didier Benoit
benoit at imnc.in2p3.fr
Mon Feb 14 22:20:28 CET 2011
Tuan,
Could you just test with my GNUmakefile?
Kind Regards,
Didier
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On Feb 14, 2011, at 9:58 PM, Tuan wrote:
> Hi Didier,
>
> That solved the problem with TROOT.h. Thanks a lot. But I still get
> the following message:
>
> tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$ make
> Entering source/arf ...
> GNUmakefile:8: *** missing separator. Stop.
> source/arf finished
> Entering source/geometry ...
> GNUmakefile:8: *** missing separator. Stop.
> source/geometry finished
> Entering source/general ...
> GNUmakefile:8: *** missing separator. Stop.
> source/general finished
> Entering source/digits_hits ...
> GNUmakefile:8: *** missing separator. Stop.
> source/digits_hits finished
> Entering source/physics ...
> GNUmakefile:8: *** missing separator. Stop.
> source/physics finished
> Creating shared library tmp/Linux-g++/Gate/libGate.so ...
> g++: *.o: No such file or directory
> make: *** [tmp/Linux-g++/Gate/libGate.so] Error 1
> tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$
>
> I don't know what to do about that.
>
> Cheers,
> Tuan Huynh
>
>
>
> On Mon, 2011-02-14 at 21:45 +0100, Didier Benoit wrote:
>> Hi Tuan,
>>
>>
>> In the GateCommon.gmk file, could you add this line: CPPFLAGS += -I
>> $(ROOTSYS)/include, for me the problem is "TROOT.h: No such file or
>> directory" a path is wrong somewhere.
>>
>>
>> Kind Regards,
>> Didier
>>
>>
>>
>> On Feb 14, 2011, at 3:55 PM, Tuan wrote:
>>
>>> Hi Didier,
>>>
>>> I just tried doing that, but it still gives the exact same error.
>>>
>>> Thanks,
>>> Tuan Huynh
>>>
>>> On Sat, 2011-02-12 at 12:00 +0100,
>>> gate-users-request at lists.opengatecollaboration.org wrote:
>>>> Send Gate-users mailing list submissions to
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>>>>
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>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. Re: Trouble installing GATE (Didier Benoit)
>>>> 2. Re: ASCII coincidence.dat (Nicolas GUIGNARD)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Fri, 11 Feb 2011 15:49:24 +0100
>>>> From: Didier Benoit <benoit at imnc.in2p3.fr>
>>>> To: Tuan <huynht4 at mcmaster.ca>
>>>> Cc: gate-users at lists.opengatecollaboration.org
>>>> Subject: Re: [Gate-users] Trouble installing GATE
>>>> Message-ID: <4D554C74.1010408 at imnc.in2p3.fr>
>>>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>>>
>>>> Hi Tuan,
>>>>
>>>> Your GATEHOME should be: /home/tuan/GATE_ROOT/gate_v6.0_p01, I
>>>> think
>>>> In your PATH variable it's better:
>>>> export PATH=$PATH:$ROOTSYS/bin:$GATEHOME/bin
>>>>
>>>> Kind Regards,
>>>> Didier
>>>>
>>>> On 02/11/2011 03:41 PM, Tuan wrote:
>>>>> Hi,
>>>>>
>>>>> I thought I already set all the environment variables in the
>>>>> env_gate.sh
>>>>> file like so:
>>>>>
>>>>> export GATEHOME=/home/tuan/GATE_ROOT
>>>>> export G4INSTALL=/home/tuan/GATE_ROOT/geant4.9.2.p04
>>>>> export G4VERSION=9.2
>>>>> export ROOTSYS=/home/tuan/GATE_ROOT/root
>>>>> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:
>>>>> $ROOTSYS/lib:/home/tuan/GATE_ROOT/2.0.4.2/lib
>>>>> export PATH=$PATH:$ROOTSYS/lib:$GATEHOME/bin/$G4SYSTEM
>>>>>
>>>>> Is that incorrect? Is there something else I'm missing?
>>>>>
>>>>> Thanks,
>>>>> Tuan Huynh
>>>>>
>>>>>
>>>>>> Message: 5
>>>>>> Date: Thu, 10 Feb 2011 21:14:19 +0100
>>>>>> From: Alexandre Dupas<alexandre.dupas at gmail.com>
>>>>>> To: gate-users at lists.opengatecollaboration.org
>>>>>> Subject: Re: [Gate-users] Trouble installing GATE
>>>>>> Message-ID:
>>>>>> <AANLkTikWpT8beyrv0NxHwCPGcDFcya7zXTEfRN_Mb3jQ at mail.gmail.com>
>>>>>> Content-Type: text/plain; charset=UTF-8
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> Actually, you have to define some environment variables to
>>>>>> allow the
>>>>>> build system to retrieve the root install directory.
>>>>>>
>>>>>> The main variable is ROOTSYS that you can define using
>>>>>>
>>>>>> export ROOTSYS=/path/to/root/installation/directory
>>>>>>
>>>>>> See for more details the "Setting environment variable"
>>>>>> section of the
>>>>>> following page :
>>>>>> http://minos.phy.bnl.gov/software/rug/rug26.html
>>>>>>
>>>>>> I hope this help,
>>>>>>
>>>>>> Best regards,
>>>>>> Alexandre
>>>>>> --
>>>>>> Alexandre Dupas
>>>>>> Postdoctoral Research Fellow
>>>>>> INSERM U698, Bich?t M?decine Nucl?aire
>>>>>>
>>>>>> 2011/2/10 Tuan<huynht4 at mcmaster.ca>:
>>>>>>> Hi,
>>>>>>>
>>>>>>> ? ? I. I've been trying to install GATE on a new
>>>>>>> system. ?I've followed
>>>>>>> ? ? ? ?the instructions on the Installation Guide to the
>>>>>>> letter but I
>>>>>>> ? ? ? ?keep getting this error when I use make:
>>>>>>>
>>>>>>> tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$ source
>>>>>>> env_gate.sh
>>>>>>>
>>>>>>> The current value of G4INSTALL
>>>>>>> is: /home/tuan/GATE_ROOT/geant4.9.2.p04
>>>>>>> The current value of G4VERSION is: 9.2
>>>>>>>
>>>>>>> Launching Geant4 configuration
>>>>>>> script /home/tuan/GATE_ROOT/geant4.9.2.p04/env.sh
>>>>>>>
>>>>>>> On this machine the G4SYSTEM=Linux-g++
>>>>>>> On this machine the
>>>>>>> G4INSTALL=/home/tuan/GATE_ROOT/geant4.9.2.p04
>>>>>>> On this machine the
>>>>>>> G4INCLUDE=/home/tuan/GATE_ROOT/geant4.9.2.p04/include/
>>>>>>> On this machine the
>>>>>>> G4LIB=/home/tuan/GATE_ROOT/geant4.9.2.p04/lib
>>>>>>> On this machine the
>>>>>>> G4LEVELGAMMADATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/PhotonEvaporation2.0
>>>>>>> On this machine the
>>>>>>> G4RADIOACTIVEDATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/RadioactiveDecay3.2
>>>>>>> On this machine the
>>>>>>> G4LEDATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/G4EMLOW6.2
>>>>>>> On this machine the
>>>>>>> G4NEUTRONHPDATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/G4NDL3.13
>>>>>>> On this machine the
>>>>>>> G4ABLADATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/G4ABLA3.0
>>>>>>> On this machine the
>>>>>>> CLHEP_BASE_DIR=/home/tuan/GATE_ROOT/2.0.4.2
>>>>>>> On this machine the
>>>>>>> CLHEP_INCLUDE_DIR=/home/tuan/GATE_ROOT/2.0.4.2/include
>>>>>>> On this machine the
>>>>>>> CLHEP_LIB_DIR=/home/tuan/GATE_ROOT/2.0.4.2/lib
>>>>>>> On this machine the CLHEP_LIB=CLHEP
>>>>>>> On this machine the G4UI_USE_TCSH=1
>>>>>>> On this machine the G4VIS_BUILD_OPENGLX_DRIVER=1
>>>>>>> On this machine the G4VIS_USE_OPENGLX=1
>>>>>>> On this machine the XMFLAGS=
>>>>>>> On this machine the XMLIBS=
>>>>>>> On this machine the XMFLAGS=
>>>>>>> On this machine the XAWFLAGS=
>>>>>>> On this machine the XAWLIBS=
>>>>>>> On this machine the G4LIB_BUILD_STATIC=1
>>>>>>> On this machine the G4LIB_USE_GRANULAR=1
>>>>>>>
>>>>>>> Configuring GATE options
>>>>>>>
>>>>>>> G4WORKDIR set to .
>>>>>>> G4TMP set to ./tmp
>>>>>>> G4BIN set to ./bin
>>>>>>> Data analysis and output features enabled
>>>>>>> Ascii data output enabled
>>>>>>> Transport and generation of optical photons is disabled
>>>>>>> Checking your LD_LIBRARY_PATH variable...
>>>>>>> ?==> OK: /home/tuan/GATE_ROOT/root/lib is already in your
>>>>>>> LD_LIBRARY_PATH
>>>>>>> Use of ROOT enabled
>>>>>>> ROOT real-time plotter disabled
>>>>>>> LMF data output disabled
>>>>>>> ECAT7 data output disabled
>>>>>>> GATEHOME is set to /home/tuan/GATE_ROOT
>>>>>>> Checking your path variable...
>>>>>>> ?==> OK: /home/tuan/GATE_ROOT/bin/Linux-g++ added to your
>>>>>>> path variable
>>>>>>> Checking your LD_LIBRARY_PATH variable...
>>>>>>> ?==> OK: /home/tuan/GATE_ROOT/tmp/Linux-g++/Gate added to
>>>>>>> your path
>>>>>>> variable
>>>>>>> G4VERSION9_2 is set: GATE is compatible with the geant4
>>>>>>> version 9.2
>>>>>>>
>>>>>>> Done
>>>>>>>
>>>>>>> tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$ make
>>>>>>> Making dependency for file Gate.cc ...
>>>>>>> ./source/physics/include/GateSourcePhaseSpace.hh:14: fatal
>>>>>>> error:
>>>>>>> TROOT.h: No such file or directory
>>>>>>> compilation terminated.
>>>>>>> Entering source/arf ...
>>>>>>> GNUmakefile:8: *** missing separator. ?Stop.
>>>>>>> source/arf finished
>>>>>>> Entering source/geometry ...
>>>>>>> GNUmakefile:8: *** missing separator. ?Stop.
>>>>>>> source/geometry finished
>>>>>>> Entering source/general ...
>>>>>>> GNUmakefile:8: *** missing separator. ?Stop.
>>>>>>> source/general finished
>>>>>>> Entering source/digits_hits ...
>>>>>>> GNUmakefile:8: *** missing separator. ?Stop.
>>>>>>> source/digits_hits finished
>>>>>>> Entering source/physics ...
>>>>>>> GNUmakefile:8: *** missing separator. ?Stop.
>>>>>>> source/physics finished
>>>>>>> Creating shared library tmp/Linux-g++/Gate/libGate.so ...
>>>>>>> g++: *.o: No such file or directory
>>>>>>> make: *** [tmp/Linux-g++/Gate/libGate.so] Error 1
>>>>>>> tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$
>>>>>>>
>>>>>>> It seems like Root wasn't installed properly so I've tried
>>>>>>> reinstalling
>>>>>>> it a few times (different versions as well) to no
>>>>>>> avail. ?What could be
>>>>>>> the problem?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Tuan Huynh
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>
>>>>
>>>> --
>>>> ----------------------------------------------------------------
>>>> Didier BENOIT, GATE Engineer
>>>>
>>>> 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
>>>> 91405 ORSAY Cedex
>>>>
>>>> T?l : (33) 1 69 15 68 76
>>>> E-mail : benoit at imnc.in2p3.fr
>>>> http://www.imnc.in2p3.fr
>>>> ----------------------------------------------------------------
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Fri, 11 Feb 2011 15:59:32 +0100
>>>> From: Nicolas GUIGNARD <nicolas.guignard8 at gmail.com>
>>>> To: Marcin Balcerzyk <m.balcerzyk at pluri.ucm.es>
>>>> Cc: gate-users at lists.opengatecollaboration.org
>>>> Subject: Re: [Gate-users] ASCII coincidence.dat
>>>> Message-ID:
>>>> <AANLkTin41zR6U9ag=nsphyxuRi8Y2y1VsFLaNxP4TJYE at mail.gmail.com>
>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>>
>>>> Hello Marcin
>>>> many many thanks for your reply and information.
>>>> Nicolas
>>>>
>>>> On Wed, Feb 9, 2011 at 11:28 AM, Marcin Balcerzyk
>>>> <m.balcerzyk at pluri.ucm.es>wrote:
>>>>
>>>>> Dear Nicolas.
>>>>>
>>>>>
>>>>>
>>>>> Coincidence.dat and other ascii files have column order
>>>>> described in Users
>>>>> Guide. Its order depends very much on the design of your
>>>>> scanner, so there
>>>>> is no universal naming.
>>>>>
>>>>>
>>>>>
>>>>> In my case of scanner I have for Singles.dat the following
>>>>> columns and
>>>>> first row of data
>>>>>
>>>>> *IDRun*
>>>>>
>>>>> *IDEvent*
>>>>>
>>>>> *IDSource*
>>>>>
>>>>> *AnihX*
>>>>>
>>>>> *AnihY*
>>>>>
>>>>> *AnihZ*
>>>>>
>>>>> *VolID*
>>>>>
>>>>> *VolID2*
>>>>>
>>>>> *VolID3*
>>>>>
>>>>> *VolID4*
>>>>>
>>>>> *VolID5*
>>>>>
>>>>> *VolID6*
>>>>>
>>>>> *TimeStamp*
>>>>>
>>>>> *EnergyDep*
>>>>>
>>>>> *EventX*
>>>>>
>>>>> *EventY*
>>>>>
>>>>> *EventZ*
>>>>>
>>>>> *ComptPhan*
>>>>>
>>>>> *ComptDet*
>>>>>
>>>>> *ReyPhan*
>>>>>
>>>>> *ReyDet*
>>>>>
>>>>> *ComptPhanName*
>>>>>
>>>>> *RayPhanName*
>>>>>
>>>>> 0
>>>>>
>>>>> 5
>>>>>
>>>>> 0
>>>>>
>>>>> -6.26E+00
>>>>>
>>>>> -2.27E+00
>>>>>
>>>>> 3.57E+00
>>>>>
>>>>> 0
>>>>>
>>>>> 5
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 1.23E-06
>>>>>
>>>>> 5.75E-01
>>>>>
>>>>> -4.19E+01
>>>>>
>>>>> -4.05E+01
>>>>>
>>>>> -1.88E+01
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> NULL
>>>>>
>>>>> NULL
>>>>>
>>>>>
>>>>>
>>>>> For coincidence.dat it is first for 1st detector, than for 2nd
>>>>> (from same
>>>>> IDEVENT you can see it?s a true coincidence):
>>>>>
>>>>> *1IDRun*
>>>>>
>>>>> *1IDEvent*
>>>>>
>>>>> *1IDSource*
>>>>>
>>>>> *1AnihX*
>>>>>
>>>>> *1AnihY*
>>>>>
>>>>> *1AnihZ*
>>>>>
>>>>> *1TimeStamp*
>>>>>
>>>>> *1EnergyDep*
>>>>>
>>>>> *1EventX*
>>>>>
>>>>> *1EventY*
>>>>>
>>>>> *1EventZ*
>>>>>
>>>>> *1VolID1*
>>>>>
>>>>> *1VolID2*
>>>>>
>>>>> *1VolID3*
>>>>>
>>>>> *1VolID4*
>>>>>
>>>>> *1VolID5*
>>>>>
>>>>> *1VolID6*
>>>>>
>>>>> *1ComptPhan*
>>>>>
>>>>> *1ComptDet*
>>>>>
>>>>> *1ReyPhan*
>>>>>
>>>>> *1ReyDet*
>>>>>
>>>>> *1ScannAx*
>>>>>
>>>>> *1ScannAng*
>>>>>
>>>>> *2IDRun*
>>>>>
>>>>> *2IDEvent*
>>>>>
>>>>> *2IDSource*
>>>>>
>>>>> *2AnihX*
>>>>>
>>>>> *2AnihY*
>>>>>
>>>>> *2AnihZ*
>>>>>
>>>>> *2TimeStamp*
>>>>>
>>>>> *2EnergyDep*
>>>>>
>>>>> *2EventX*
>>>>>
>>>>> *2EventY*
>>>>>
>>>>> *2EventZ*
>>>>>
>>>>> *2VolID1*
>>>>>
>>>>> *2VolID2*
>>>>>
>>>>> *2VolID3*
>>>>>
>>>>> *2VolID4*
>>>>>
>>>>> *2VolID5*
>>>>>
>>>>> *2VolID6*
>>>>>
>>>>> *2ComptPhan*
>>>>>
>>>>> *2ComptDet*
>>>>>
>>>>> *2ReyPhan*
>>>>>
>>>>> *2ReyDet*
>>>>>
>>>>> *2ScannAx*
>>>>>
>>>>> *2ScannAng*
>>>>>
>>>>> 0
>>>>>
>>>>> 154
>>>>>
>>>>> 0
>>>>>
>>>>> 5.18E+00
>>>>>
>>>>> -1.93E+00
>>>>>
>>>>> -1.74E+00
>>>>>
>>>>> 4.15E-05
>>>>>
>>>>> 4.99E-01
>>>>>
>>>>> 3.29E+01
>>>>>
>>>>> -5.39E+01
>>>>>
>>>>> 6.66E+00
>>>>>
>>>>> 0
>>>>>
>>>>> 3
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0.00E+00
>>>>>
>>>>> 0.00E+00
>>>>>
>>>>> 0
>>>>>
>>>>> 154
>>>>>
>>>>> 0
>>>>>
>>>>> 5.18E+00
>>>>>
>>>>> ########
>>>>>
>>>>> ########
>>>>>
>>>>> 4.15E-05
>>>>>
>>>>> 4.83E-01
>>>>>
>>>>> -2.97E+01
>>>>>
>>>>> 6.15E+01
>>>>>
>>>>> -1.29E+01
>>>>>
>>>>> 0
>>>>>
>>>>> 7
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0
>>>>>
>>>>> 0.00E+00
>>>>>
>>>>> 0.00E+00
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> I hope that helps. Surely format of two tables above is lost in
>>>>> Gate list.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Marcin Balcerzyk,
>>>>>
>>>>> Unidad Ciclotron,
>>>>>
>>>>> Centro Nacional de Aceleradores,
>>>>>
>>>>> Universidad de Sevilla,
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Message: 3
>>>>>
>>>>> Date: Tue, 8 Feb 2011 15:18:04 +0100
>>>>>
>>>>> From: Nicolas GUIGNARD <nicolas.guignard8 at gmail.com>
>>>>>
>>>>> To: gate-users at lists.opengatecollaboration.org
>>>>>
>>>>> Subject: Re: [Gate-users] ASCII coincidence.dat analysis
>>>>>
>>>>> Message-ID:
>>>>>
>>>>> <AANLkTimG_2=swc-UpfEyFUkcCTuxmOiCuMWPqOam0p
>>>>> +c at mail.gmail.com>
>>>>>
>>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>>>
>>>>>
>>>>>
>>>>> Hello dear All
>>>>>
>>>>> I have seen lot of published literature using GATE and its
>>>>> output
>>>>> processing in forms of sinogram.That means persons using GATE
>>>>> have procesed
>>>>> the GATE ACSII files.But I am really so much surprised why
>>>>> people don't
>>>>> answer, share or guide how to do this for a naive user.
>>>>>
>>>>>
>>>>>
>>>>> Thanks
>>>>>
>>>>> Nicolas
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> Gate-users mailing list
>>>> Gate-users at lists.opengatecollaboration.org
>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>
>>>> End of Gate-users Digest, Vol 57, Issue 12
>>>> ******************************************
>>>
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>
>>
>> ----------------------------------------------------------------
>> Didier BENOIT, GATE Engineer
>> 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 68 76
>> E-mail : benoit at imnc.in2p3.fr
>> http://www.imnc.in2p3.fr
>> ----------------------------------------------------------------
>>
>>
>>
>>
>
>
----------------------------------------------------------------
Didier BENOIT, GATE Engineer
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 68 76
E-mail : benoit at imnc.in2p3.fr
http://www.imnc.in2p3.fr
----------------------------------------------------------------
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