[Gate-users] Trouble installing GATE

Mon Feb 14 15:55:27 CET 2011

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
> >
> >
> >
> >
> >
> 
> 
> ------------------------------
> 
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