[Gate-users] Problems with optical transport

Jenny Nilsson jenny.nilsson at radfys.gu.se
Tue Nov 22 13:42:16 CET 2011 

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>

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