GATE

Description
	GATE, the "Geant4 Application for Emission Tomography", incorporates the Geant4 libraries in a modular, versatile, and scripted simulation toolkit which is adapted to the field of nuclear medicine, specifically in the area of PET (Positron Emission Tomography) or SPECT (Single Photon Emission Computer Tomography) simulation. GATE allows the accurate description of time-dependent phenomena such as source or detector movement and source decay kinetics.
Site	Version (Latest: v6.1)	Notes
ngs.rl.ac.uk	v3.1.1, v4.0.0	64 bit

License

Gate is distributed freely for academics, under an LGPL license. To use Gate on the NGS (RAL node) you should register with the OpenGate collaboration first. WIthout registration you cannot access the documentation or examples.

Running the GATE on the NGS (General)

There a multiple ways in which jobs can be launched on the NGS

• Submission Using UI/WMS

This service is coming soon

• NGS Web Portal Submission

After logging in to the NGS Portal, select the "GATE" template under the " BioMedical" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus

  To run Gate on the NGS your input macro file must turn off all graphics. For example in the SPECT benchmark the graphics windows in the visu.mac file are disabled as below:

  # VISUALISATION
  /vis/disable
  #/control/execute visu.mac
  

  The output file is defined by the user and has to be given when the job is submitted, i.e (stdout=StdOut.txt).

  Gate is a serial application and only requires one processor.

  The string 'xxx' in the subsequent commands is to be replaced with your id on NGS.

  You can also create a directory within your home directory (named gate in the following examples) which will be the working directory.

  Any input files (eg SPECTbenchmark.mac) required should be copied on NGS (using gsiscp) in the appropriate directory (/home/xxx/gate in our example).

  • Example run of the Gate SPECT benchmark on the NGS:

  To submit a serial Gate job on the NGS use the following command (one line without the '\' characters):

  globus-job-submit ngs.rl.ac.uk/jobmanager-lsf \
  -x '& (jobtype=single)(arguments= SPECTbench.mac) \
  (directory=/home/xxx/gate) (stderr=/home/xxx/gate/StdErr.txt) \
  (stdout=/home/xxx/gate/StdOut.txt)' /usr/ngs/GATE_4_0_0

  Replace GATE_4_0_0 by GATE_3_1 to run v3.1.1

  If submitting from ngs.rl.ac.uk this string can be shortened by :

  cd <run directory>
  export GATEVERSION=4_0_0 (or 3_1)
  run_gate SPECTbench.mac

  Or to submit to the local batch system on ngs.rl.ac.uk:

  cd <run directory>
  export GATEVERSION=4_0_0 (or 3_1)
  run_gate_lsf SPECTbench.mac

  We also provide a utility script to submit many runs. Provided that each macro file is in a separate directory prefixed 'run_' below "top-run-directory" then:

  cd <top-run-directory>
  export GATEVERSION=4_0_0 (or 3_1)
  run_all_gate

  Will cd into each 'run_*' directory and submit the macro file(s) there as a separate job.

  • Example run of the ROOT post-simulation analysis on the NGS:

  Although Root can be used as an interactive tool, for long analyses it should be used in batch mode. Here is an example of how to run the Root analysis on the SPECT benchmark over the grid:

  globus-job-submit ngs.rl.ac.uk/jobmanager-lsf \
  -x '& (jobtype=single)(arguments= root -b -q benchSPECT.C) \
  (directory=/home/xxx/gate) (stderr=/home/xxx/gate/RootErr.txt) \
  (stdout=/home/xxx/gate/RootOut.txt)' /usr/ngs/ROOT_5_14

  If you wish to run any of the other root package binaries, replace 'root' by the binary name in the arguments section of the above command.

   

  Module	Executable
  libCLHEP/2.0.2.3	/apps/libs/CLHEP/CLHEP-2.0.2.3/lib/libCLHEP.a, libCLHEP.so
  libCLHEP/2.0.3.2	/apps/libs/CLHEP/CLHEP-2.0.3.2/lib/libCLHEP.a, libCLHEP.so
  root/5.12	/apps/Root/5.12/root/bin/root
  root/5.14	/apps/Root/5.14/root/bin/root
  GATE/3.1.1	/apps/gate/gate_v3.1.1/bin/Linux-g++/Gate
  GATE/4.0.0	/apps/gate/gate_v4.0.0/bin/Linux-g++/Gate

  Compilation Information for ngs.rl.ac.uk 

  The 3.1.1 version of Gate is compiled (using Gcc 3.4.6) against the following library versions:
  CLHEP 2.0.2.3
  GEANT4 8.1.p02 (With G4EMLOW4.2 data and openGL libraries only)
  Root 5.12
  

  The 4.0.0 version of Gate is compiled (using Gcc 3.4.6) against the following library versions:
  CLHEP 2.0.3.2
  GEANT4 9.1.p02
  Root 5.14
  

  If you need information on how this application was compiled please contact the NGS support centre.

  Further Information 

  • OpenGate Home Page
  • Gate's Manuals. However you need to register with OpenGateto view them.
  • CLHEP - A Class Library for High Energy Physics
  • GEANT4 Web Site
  • ROOT website