[Gate-users] Gate v7.1 installation on Mac OSX

Pietrzyk, Uwe u.pietrzyk at fz-juelich.de
Tue Sep 15 11:08:30 CEST 2015 

Hi Pete,

I am not an expert in all this installation issues, but I cannot find
an obvious error you might have made.
Now let me ask, what exactly is the error you find? I didn’t fully
understand your first eMail and simply responded to your question
on starting or adding a script file.
Note, to check if the installation was successful is easiest done by
starting Gate as I wrote in my first response AND (!!) also to run
the benchmarks and/or examples provided with the GATE-
distribution.
Feel free to let us know what you find and whether it works.

Kind regards,

Uwe Pietrzyk
/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
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&
Bergische Universität Wuppertal
Fachbereich C - Physik / D.08.01
Gaußstr. 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/>
----------------------------------------------------------------------/

On 15 Sep 2015, at 10:20, Pete Z. Wu <pzw at ns.ph.liv.ac.uk<mailto:pzw at ns.ph.liv.ac.uk>> wrote:

Hi Uwe,

Thanks for the prompt response to my post. To clarify, I installed Gate (version 7.1) from source code. The commands used during the configuration process are as follows:

cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install -DGATE_DOWNLOAD_BENCHMARKS_DATA=ON /usr/local/gate_v7.1
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install -DGATE_DOWNLOAD_EXAMPLES_DATA=OFF /usr/local/gate_v7.1
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install -DGATE_USE_ECAT7=OFF /usr/local/gate_v7.1
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install -DGATE_USE_GEANT4_UIVIS=ON /usr/local/gate_v7.1
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install -DGATE_USE_GPU=OFF /usr/local/gate_v7.1
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install -DGATE_USE_LMF=OFF /usr/local/gate_v7.1
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install -DGATE_USE_OPTICAL=OFF /usr/local/gate_v7.1
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install -DGATE_USE_SYSTEM_CLHEP=OFF /usr/local/gate_v7.1


After setting up all the flags as shown i.e USE_GPU=OFF etc.  I ran the “make –j4” command and “make install” command in sequence as shown below. I did not get any error messages during these two stages either.

make -j4
make install

Now, as I understand if these two stages are successful (as it appears to be in my case) the installation should be OK. However, when I try to run Gate from the terminal I get an error message. I should be grateful if you could confirm to me that the procedure I have listed above in this email is correct. I should also mention that both ROOT and GEANT4 are working on my macbook.

Many thanks,
Pete





Quoting "Pietrzyk, Uwe" <u.pietrzyk at fz-juelich.de<mailto:u.pietrzyk at fz-juelich.de>>:

Hi Pete,

nit sure, whether I understood your question correctly, but the following
lines I copied from a terminal window may be helpful for you:

medmac23 1 --> cd /Applications/gate_v7.1-install/bin
medmac23 2 --> ll
total 15368
-rwxr-xr-x  1 upietrzyk  admin  7860824 May  8 14:23 Gate*
-rwxr-xr-x@ 1 upietrzyk  admin      113 May  8 14:37 env_gate.csh*

medmac23 3 --> pwd
/Applications/gate_v7.1-install/bin

medmac23 4 --> more env_gate.csh
source /Applications/geant4.10.01-install/bin/geant4.csh
setenv PATH ${PATH}:/Applications/gate_v7.1-install/bin
medmac23 5 -->

medmac23 5 --> source env_gate.csh

medmac23 8 --> which Gate
./Gate

medmac23 7 --> Gate
[G4]
[G4] *************************************************************
[G4]  Geant4 version Name: geant4-10-01    (5-December-2014)
[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_v7.1
[Core-0]                     Copyright : OpenGATE Collaboration
[Core-0]                     Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0]                     Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0]                     WWW : http://www.opengatecollaboration.org
[Core-0] **********************************************************************
[Core-0]
[Core-0] You are using Geant4 version 10.1.0
Idle> exit
Graphics systems deleted.
Visualization Manager deleting...


Kind regards and best wishes,

Uwe Pietrzyk

/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk at fz-juelich.de<mailto:U.Pietrzyk at fz-juelich.de><mailto:U.Pietrzyk at fz-juelich.de>
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fachbereich C - Physik / D.08.01
Gaußstr. 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><mailto:Uwe.Pietrzyk at physik.uni-wuppertal.de>
http://www.medizinphysik.uni-wuppertal.de<http://www.medizinphysik.uni-wuppertal.de/>
----------------------------------------------------------------------/

On 15 Sep 2015, at 08:06, Pete Z. Wu <pzw at ns.ph.liv.ac.uk<mailto:pzw at ns.ph.liv.ac.uk><mailto:pzw at ns.ph.liv.ac.uk>> wrote:

Dear GATE expert,

I’m new to GATE. I recently installed gate_v7.1 on my MacBook Pro. During the configuration, building and installation stages I did not get any error messages, everything seams to be done quite smoothly. After the installation was completed I needed to write the source script i.e. .sh file into my .bashrc file. However, I’m not sure where this file should be. It does not appear to be in either the installation or build directories i.e. gate_v7.1-build or gate_v7.1-install.

I should be very grateful if you would let me know explicitly how I should source the .sh script in my .bashrc file.

Many thanks,
Pete

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