[Gate-users] Problems with optical transport

Didier Benoit benoit at imnc.in2p3.fr
Wed Nov 23 15:46:08 CET 2011 

Hi Jenny,

Have you tried to launch the optical transport example being in the 
folder /applications/gate_v6.1/examples/example_OPTICAL? (And only type 
the command Gate opticalMacro.mac).

In fact each macros are in the folder 
/applications/gate_v6.1/examples/example_OPTICAL/macro, so if you launch 
Gate /applications/gate_v6.1/examples/example_OPTICAL/opticalMacro.mac, 
your files macro/*.mac are not found by GATE. I think it's the problem.

Kind regards,
Didier

On 11/22/2011 01:42 PM, Jenny Nilsson wrote:
> Hello,
> I’m running Gate on a Mac OS X Snow Leopard.
> I managed to install and run Gate, but then needed to use optical transport as well. I then did the following.
> Used MacPort to get the latest version of libxml2-dev.
> Changed env_gate.sh, env_gate.csh
> unsetenv GATE_USE_OPTICAL
> # setenv GATE_USE_OPTICAL 1
> if ( ${?GATE_USE_OPTICAL} )
> to
> # unsetenv GATE_USE_OPTICAL
> setenv GATE_USE_OPTICAL 1
> if ( ${?GATE_USE_OPTICAL} )
> Then, in the Gate directory
> source env_gate.sh
> make
> Below is the output I get when starting up X11 and later on running the optical example. There is something wrong but I can’t figure it out, any help is much appreciated. I’m no Mac expert so I might have missed something very obvious.
> Best regards
> Jenny Nilsson
>
> Starting up X11 I get the following
> 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 enabled
> Checking your LD_LIBRARY_PATH variable...
>   ==>  OK: /Applications/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 /Applications/gate_v6.1
> Checking your path variable...
>   ==>  OK: /Applications/gate_v6.1/bin/Darwin-g++ added to your path variable
> Checking your LD_LIBRARY_PATH variable...
>   ==>  OK: /Applications/gate_v6.1/tmp/Darwin-g++/Gate added to your path variable
> G4VERSION9_3 is set: GATE is compatible with the GEANT4 version 9.3 and 9.4
> Done
>
> And when running the optical example i got the following result
>
> On this machine the G4SYSTEM=Darwin-g++
> On this machine the G4INSTALL=/Applications/geant4.9.4.p02
> On this machine the G4LIB=/Applications/geant4.9.4.p02/lib
> On this machine the G4LEVELGAMMADATA=/Applications/geant4.9.4.p02/data/PhotonEvaporation2.1
> On this machine the G4RADIOACTIVEDATA=/Applications/geant4.9.4.p02/data/RadioactiveDecay3.3
> On this machine the G4LEDATA=/Applications/geant4.9.4.p02/data/G4EMLOW6.19
> On this machine the G4NEUTRONHPDATA=/Applications/geant4.9.4.p02/data/G4NDL3.14
> On this machine the G4ABLADATA=/Applications/geant4.9.4.p02/data/G4ABLA3.0
> On this machine the G4REALSURFACEDATA=/Applications/geant4.9.4.p02/data/RealSurface1.0
> On this machine the G4NEUTRONXSDATA=/Applications/geant4.9.4.p02/data/G4NEUTRONXS1.0
> On this machine the G4PIIDATA=/Applications/geant4.9.4.p02/data/G4PII1.2
> On this machine the CLHEP_BASE_DIR=/Applications/CLHEP
> On this machine the CLHEP_INCLUDE_DIR=/Applications/CLHEP/include
> On this machine the CLHEP_LIB_DIR=/Applications/CLHEP/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_BUILD_RAYTRACERX_DRIVER=1
> On this machine the G4VIS_USE_OPENGLX=1
> On this machine the G4VIS_USE_RAYTRACERX=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_SHARED=1
>
> The current value of G4INSTALL is: /Applications/geant4.9.4.p02
> The current value of G4VERSION is: 9.4
>
> Launching Geant4 configuration script /Applications/geant4.9.4.p02/env.sh
>
> On this machine the G4SYSTEM=Darwin-g++
> On this machine the G4INSTALL=/Applications/geant4.9.4.p02
> On this machine the G4LIB=/Applications/geant4.9.4.p02/lib
> On this machine the G4LEVELGAMMADATA=/Applications/geant4.9.4.p02/data/PhotonEvaporation2.1
> On this machine the G4RADIOACTIVEDATA=/Applications/geant4.9.4.p02/data/RadioactiveDecay3.3
> On this machine the G4LEDATA=/Applications/geant4.9.4.p02/data/G4EMLOW6.19
> On this machine the G4NEUTRONHPDATA=/Applications/geant4.9.4.p02/data/G4NDL3.14
> On this machine the G4ABLADATA=/Applications/geant4.9.4.p02/data/G4ABLA3.0
> On this machine the G4REALSURFACEDATA=/Applications/geant4.9.4.p02/data/RealSurface1.0
> On this machine the G4NEUTRONXSDATA=/Applications/geant4.9.4.p02/data/G4NEUTRONXS1.0
> On this machine the G4PIIDATA=/Applications/geant4.9.4.p02/data/G4PII1.2
> On this machine the CLHEP_BASE_DIR=/Applications/CLHEP
> On this machine the CLHEP_INCLUDE_DIR=/Applications/CLHEP/include
> On this machine the CLHEP_LIB_DIR=/Applications/CLHEP/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_BUILD_RAYTRACERX_DRIVER=1
> On this machine the G4VIS_USE_OPENGLX=1
> On this machine the G4VIS_USE_RAYTRACERX=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_SHARED=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 enabled
> Checking your LD_LIBRARY_PATH variable...
>   ==>  OK: /Applications/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 /Applications/gate_v6.1
> Checking your path variable...
>   ==>  OK: /Applications/gate_v6.1/bin/Darwin-g++ added to your path variable
> Checking your LD_LIBRARY_PATH variable...
>   ==>  OK: /Applications/gate_v6.1/tmp/Darwin-g++/Gate added to your path variable
> G4VERSION9_3 is set: GATE is compatible with the GEANT4 version 9.3 and 9.4
>
> Done
>
> bash-3.2$ gate
> [G4]
> [G4] *************************************************************
> [G4]  Geant4 version Name: geant4-09-04-patch-02    (24-June-2011)
> [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_v6.1
> [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]
> Idle>  control/execute /applications/gate_v6.1/examples/example_OPTICAL/opticalMacro.mac
> /tracking/storeTrajectory 1
> WARNING: Trajectory storing has been requested.  This action may be
>    reversed with "/tracking/storeTrajectory 0".
> WARNING: The vis manager will keep up to 100 events.
>    This may use a lot of memory.
>    It may be changed with, e.g., "/vis/scene/endOfEventAction accumulate 10".
> G4PhysicalVolumeModel::Validate() called.
>    Volume of the same name and copy number ("world_phys", copy 0) still exists and is being used.
>    WARNING: This does not necessarily guarantee it's the same
>    volume you originally specified in /vis/scene/add/.
> G4PhysicalVolumeModel::Validate() called.
>    Volume of the same name and copy number ("world_phys", copy 0) still exists and is being used.
>    WARNING: This does not necessarily guarantee it's the same
>    volume you originally specified in /vis/scene/add/.
> G4PhysicalVolumeModel::Validate() called.
>    Volume of the same name and copy number ("world_phys", copy 0) still exists and is being used.
>    WARNING: This does not necessarily guarantee it's the same
>    volume you originally specified in /vis/scene/add/.
> G4PhysicalVolumeModel::Validate() called.
>    Volume of the same name and copy number ("world_phys", copy 0) still exists and is being used.
>    WARNING: This does not necessarily guarantee it's the same
>    volume you originally specified in /vis/scene/add/.
> ***** COMMAND NOT FOUND</gate/pixel/surfaces/name teflonsurf>  *****
>
> ***** Batch is interrupted!! *****
>
>
> List of Enabled processes:
>
>
>     ===  Process: Bremsstrahlung  ===
> Particle: e+
>      * Model(s):
>         -<!>  *** Warning ***<!>  No model selected!
> Particle: e-
>      * Model(s):
>         - StandardModel
>
>     ===  Process: Compton  ===
> Particle: gamma
>      * Model(s):
>         - PenelopeModel
>
>     ===  Process: ElectronIonisation  ===
> Particle: e+
>      * Model(s):
>         -<!>  *** Warning ***<!>  No model selected!
> Particle: e-
>      * Model(s):
>         - StandardModel
>
>     ===  Process: MultipleScattering  ===
> Particle: e-
>
>     ===  Process: OpticalAbsorption  ===
> Particle: opticalphoton
>
>     ===  Process: OpticalBoundary  ===
> Particle: opticalphoton
>
>     ===  Process: OpticalRayleigh  ===
> Particle: opticalphoton
>
>     ===  Process: PhotoElectric  ===
> Particle: gamma
>      * Model(s):
>         - StandardModel
>
>     ===  Process: RayleighScattering  ===
> Particle: gamma
>      * Model(s):
>         - PenelopeModel
>
>     ===  Process: Scintillation  ===
> Particle: e+
> Particle: e-
> Particle: mu+
> Particle: mu-
> Particle: tau+
> Particle: tau-
> Particle: pi+
> Particle: pi-
> Particle: kaon+
> Particle: kaon-
> Particle: sigma+
> Particle: sigma-
> Particle: proton
> Particle: anti_proton
> Particle: xi-
> Particle: anti_xi-
> Particle: anti_sigma+
> Particle: anti_sigma-
> Particle: omega-
> Particle: anti_omega-
> Particle: deuteron
> Particle: triton
> Particle: He3
> Particle: alpha
> Particle: GenericIon
> Particle: neutron
> Particle: gamma
>
>
>
>
> List of initialized processes:
>
>
>
> [Core-0] Initialization of geometry
> G4PhysicalVolumeModel::Validate() called.
>    Volume of the same name and copy number ("world_phys", copy 0) still exists and is being used.
>    WARNING: This does not necessarily guarantee it's the same
>    volume you originally specified in /vis/scene/add/.
> [Core-0] Initialization of physics
> [Core-0] Initialization of actors
> ***** COMMAND NOT FOUND</gate/digitizer/Singles/readout/setDepth 1>  *****
>
> ***** Batch is interrupted!! *****
> Pulse-processor type name 'opticaladder' was not recognised -->  insertion request must be ignored!
> Idle>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users


-- 
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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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