[Gate-users] Trouble installing GATE

Didier Benoit benoit at imnc.in2p3.fr
Mon Feb 14 21:45:47 CET 2011 

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:
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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
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----------------------------------------------------------------
Didier BENOIT, GATE Engineer
Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
Campus d’Orsay
Bâtiment 440
91406 ORSAY Cedex
 
Tél : (33) 1 69 15 68 76
E-mail : benoit at imnc.in2p3.fr
http://www.imnc.in2p3.fr
----------------------------------------------------------------

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