[Gate-users] LMF output issues

Wed Sep 22 11:52:12 CEST 2010

Hello Dounia,

I am afraid someone else has to help you with the problem of Gate V4 recognizing LMF output. On the other issue I might be able to help with a hint. I encountered the same messages as you do, i.e.

What do you want to store ?

1 : event record

  (y / n) : n

**** ERROR !!! TRY AGAIN ****

The problem is due to the “line end” character read when you finalize your input (“n”) with the “enter” key. The LMF code expects something other than “\n” after the “n”. I do not remember which file has to be modified in order to make this work, but you should do a “grep” for the text “**** ERROR !!! TRY AGAIN ****” in the LMF source directory in order to find the file and modify it accordingly. The same happens if you put “y” for “yes”, meaning that these lines of code also have to be modified. If you do so, the example will work. Please be aware that these input errors are present in several places in the examples, I remember that I gave up on modifying all files in the end. However, this should not be the cause of your problems between Gate and LMF.

Best regards,

Wolf

Dr. Wolfram Stiller

Diplom-Physiker

Universitätsklinikum Heidelberg

Abteilung für Diagnostische und Interventionelle Radiologie

Im Neuenheimer Feld 110

D-69120 Heidelberg

Germany

E-mail: wolfram.stiller at med.uni-heidelberg.de

Tel.: +49 (0) 6221 56 37240 or

       +49 (0) 6221 56 6434

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-----Ursprüngliche Nachricht-----
Von: gate-users-bounces at lists.opengatecollaboration.org [mailto:gate-users-bounces at lists.opengatecollaboration.org] Im Auftrag von dounia84 at aol.com
Gesendet: Mittwoch, 22. September 2010 10:47
An: gate-users at lists.opengatecollaboration.org
Betreff: [Gate-users] LMF output issues

 Hello Gaters,

I wrote an email yesterday about problem installing Gate with LMF, eventually I managed this. But now the problem is when I try the example given with LMF EXE_01. When I type

./EXE_01

This is what I get:

         Example 1

    Creation of your first LMF file

 This example allows you to create a complete

 binary LMF file, with .ccs extension. The values

 of generated records are not pertinent, but

 it is just a pedagogic example. The output of

 this example is called test1_ex1.ccs

 You can find in this directory test1_ex1.cch,

 the associated ascii file. You can read and/or process

 this couple of files with Example 4.

What do you want to store ?

1 : event record

  (y / n) : n

**** ERROR !!! TRY AGAIN ****

 It is like character encoding is not recognized.

Moreover Gate V4 does not recognize LMF output either (***** COMMAND NOT FOUND </gate/output/lmf/enable> *****

***** Batch is interupted!! *****)   even though LMF seems to be installed. I recomiled Gate several times after I have tried lots of version of lmf v3( with etags, the one modified by S. Burg,...)

but I still cannot use the ouput. I hope someone can help me as I am stuck at this step for months now.

Cheers,

The current value of G4INSTALL is: /home/dounia/gate_v4.0.0/geant4.9.1.p03

The current value of G4VERSION is: 9.1

Launching Geant4 configuration script /home/dounia/gate_v4.0.0/geant4.9.1.p03/env.sh

On this machine the G4SYSTEM=Linux-g++

On this machine the G4INSTALL=/home/dounia/gate_v4.0.0/geant4.9.1.p03

On this machine the G4INCLUDE=/home/dounia/gate_v4.0.0/geant4.9.1.p03/include/

On this machine the G4LIB=/home/dounia/gate_v4.0.0/geant4.9.1.p03/lib

On this machine the G4LEVELGAMMADATA=/home/dounia/gate_v4.0.0/geant4.9.1.p03/data/PhotonEvaporation2.0

On this machine the G4RADIOACTIVEDATA=/home/dounia/gate_v4.0.0/geant4.9.1.p03/data/RadioactiveDecay3.2

On this machine the G4LEDATA=/home/dounia/gate_v4.0.0/geant4.9.1.p03/data/G4EMLOW5.1

On this machine the G4NEUTRONHPDATA=/home/dounia/gate_v4.0.0/geant4.9.1.p03/data/G4NDL3.12

On this machine the G4ABLADATA=/home/dounia/gate_v4.0.0/geant4.9.1.p03/data/G4ABLA3.0

On this machine the CLHEP_BASE_DIR=/home/dounia/gate_v4.0.0/2.0.3.2/CLHEP

On this machine the CLHEP_INCLUDE_DIR=/home/dounia/gate_v4.0.0/2.0.3.2/CLHEP/include

On this machine the CLHEP_LIB_DIR=/home/dounia/gate_v4.0.0/2.0.3.2/CLHEP/lib

On this machine the CLHEP_LIB=CLHEP

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_SHARED=1

On this machine the G4LIB_BUILD_STATIC=1

On this machine the G4UI_USE_TCSH=1

LD_LIBRARY_PATH is set to include CLHEP and Geant4 libraries.

NOTE : verify that the correct path for the CLHEP library

- $CLHEP_BASE_DIR/lib - is included in the $LD_LIBRARY_PATH

variable in your environment, and no other outdated installations

of CLHEP are by chance referenced through $LD_LIBRARY_PATH and

present in your system !

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: /home/dounia/gate_v4.0.0/root/lib is already in your LD_LIBRARY_PATH

Use of ROOT enabled

ROOT real-time plotter disabled

Checking your LD_LIBRARY_PATH variable...

 ==> OK: /home/dounia/gate_v4.0.0/lmf_v3.0/lib is already in your LD_LIBRARY_PATH

LMF data output enabled

FOCUS data output enabled

ECAT7 data output enabled

GATEHOME is set to /home/dounia/gate_v4.0.0/gate_v4.0.0

Checking your path variable...

 ==> OK: /home/dounia/gate_v4.0.0/gate_v4.0.0/bin/Linux-g++ is already in your path variable

G4VERSION9 is set: GATE is compatible with the geant4 version 9.1

Done

Dounia Taleb

Imagerie medicale experimentale - Département de physique

Université de Liège - Institut de Physique, B5

B-4000 Liège 1 (Sart-Tilman) - Belgique

Tel: +32-4-3663152

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