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

Pete Z. Wu pzw at ns.ph.liv.ac.uk
Wed Sep 16 03:48:18 CEST 2015


Dear Uwe,

Sorry for the delay in responding to your email. When I run the Gate  
command in a terminal I get the following error:

pzw at machintosh$ Gate
dyld: Library not loaded: @rpath/libCore.so
   Referenced from: /usr/local/gate_v7.1-install/bin/Gate
   Reason: image not found
Trace/BPT trap: 5

However, during the installation process (i.e. during the  
configuration, build and installation processes) I DID NOT observe any  
error messages.

My installation manifest is shown below:
/usr/local/gate_v7.1-install/bin/Gate
/usr/local/gate_v7.1-install/lib/libMetaIO.a
/usr/local/gate_v7.1-install/include/localMetaConfiguration.h
/usr/local/gate_v7.1-install/include/metaArray.h
/usr/local/gate_v7.1-install/include/metaArrow.h
/usr/local/gate_v7.1-install/include/metaBlob.h
/usr/local/gate_v7.1-install/include/metaCommand.h
/usr/local/gate_v7.1-install/include/metaContour.h
/usr/local/gate_v7.1-install/include/metaDTITube.h
/usr/local/gate_v7.1-install/include/metaEllipse.h
/usr/local/gate_v7.1-install/include/metaEvent.h
/usr/local/gate_v7.1-install/include/metaFEMObject.h
/usr/local/gate_v7.1-install/include/metaForm.h
/usr/local/gate_v7.1-install/include/metaGaussian.h
/usr/local/gate_v7.1-install/include/metaGroup.h
/usr/local/gate_v7.1-install/include/metaImage.h
/usr/local/gate_v7.1-install/include/metaImageTypes.h
/usr/local/gate_v7.1-install/include/metaImageUtils.h
/usr/local/gate_v7.1-install/include/metaITKUtils.h
/usr/local/gate_v7.1-install/include/metaLandmark.h
/usr/local/gate_v7.1-install/include/metaLine.h
/usr/local/gate_v7.1-install/include/metaMesh.h
/usr/local/gate_v7.1-install/include/metaObject.h
/usr/local/gate_v7.1-install/include/metaOutput.h
/usr/local/gate_v7.1-install/include/metaScene.h
/usr/local/gate_v7.1-install/include/metaSurface.h
/usr/local/gate_v7.1-install/include/metaTransform.h
/usr/local/gate_v7.1-install/include/metaTube.h
/usr/local/gate_v7.1-install/include/metaTubeGraph.h
/usr/local/gate_v7.1-install/include/metaTypes.h
/usr/local/gate_v7.1-install/include/metaUtils.h
/usr/local/gate_v7.1-install/include/metaVesselTube.h
/usr/local/gate_v7.1-install/include/metaIOConfig.h

My .bashrc file setting:
PATH=$PATH:/usr/local/gate_v7.1-install/bin

Your help in resolving my problem is greatly appreciated.

Kind regards,
Pete

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

> 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
> Mobil: +49-162-103-4871
> eMail: 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>
> 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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