Updated: 15 September 2024
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This guide is largely derived from https://opentopas.readthedocs.io/en/latest/getting-started/Debian.html#. It is recommended to visit the page for more detailed explanation of each [Step X] . |
1. Load required modules and set environment variables [Step 1-4]
Paste the below lines into your terminal. (Do NOT put these directly in ~/.bashrc.)
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module purge module load expat/2.5.0 module load X11/20231019-cpeCray-23.03 module load libGLU/9.0.3-cpeCray-23.03 module load HarfBuzz/8.2.2-cpeCray-23.03 module load CMake/3.26.4 export CC=cc CXX=CC FC=ftn F77=ftn F90=ftn |
2. Download Geant4 [Step 5]
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mkdir $HOME/Applications/GEANT4 cd $HOME/Applications/GEANT4 wget https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.3/geant4-v11.1.3.tar.gz tar -zxf geant4-v11.1.3.tar.gz |
3. Install Geant4 [Step 7]
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cd $HOME/Applications/GEANT4/
rm -rf geant4-install geant4-build
mkdir geant4-{build,install}
cd geant4-build
cmake ../geant4-v11.1.3 -DGEANT4_INSTALL_DATA=OFF -DGEANT4_BUILD_MULTITHREADED=ON -DCMAKE_INSTALL_PREFIX=../geant4-install -DGEANT4_USE_QT=OFF -DGEANT4_USE_OPENGL_X11=ON -DGEANT4_USE_RAYTRACER_X11=ON
make -j8 install
cd $HOME/Applications/GEANT4/geant4-install
ln -s lib64 lib |
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4. Download G4DATA [Step 6]
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As of 10 September 2024, there is a connection issue between transfer.lanta.nstda.or.th and https://cern.ch/.Therefore, G4DATA was previously downloaded by ThaiSC admin and temporarily made available at |
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cd $HOME/Applications/GEANT4/ cp -r /project/common/G4DATA . |
5. Download OpenTOPAS [Step 8.1]
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mkdir $HOME/Applications/TOPAS cd $HOME/Applications/TOPAS git clone https://github.com/OpenTOPAS/OpenTOPAS.git |
6. Install GDCM [Step 8.2-8.3]
If $HOME/Applications/GDCM already exists, rename it to another name such as mv $HOME/Applications/GDCM $HOME/Applications/GDCM-OLD before proceed.
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mkdir $HOME/Applications/GDCM
cd $HOME/Applications/TOPAS/OpenTOPAS
mv gdcm-2.6.8.tar.gz ../../GDCM
cd ../../GDCM
tar -zxf gdcm-2.6.8.tar.gz
rm -rf gdcm-install gdcm-build
mkdir gdcm-{build,install}
cd gdcm-build
cmake ../gdcm-2.6.8 -DGDCM_BUILD_SHARED_LIBS=ON -DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF -DCMAKE_INSTALL_PREFIX=../gdcm-install
make -j8 install |
7. Install OpenTOPAS [Step 8.4]
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cd $HOME/Applications/TOPAS
rm -rf OpenTOPAS-install OpenTOPAS-build
mkdir OpenTOPAS-{build,install}
cd OpenTOPAS-build
export Geant4_DIR=$HOME/Applications/GEANT4/geant4-install
export GDCM_DIR=$HOME/Applications/GDCM/gdcm-install
cmake ../OpenTOPAS -DCMAKE_INSTALL_PREFIX=../OpenTOPAS-install
make -j8 install |
8. Create a wrapper script of topas [Step 9.1.b]
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mkdir $HOME/Applications/shellScripts cd $HOME/Applications/shellScripts cat << Eof > topas #!/bin/bash module purge module load expat/2.5.0 module load X11/20231019-cpeCray-23.03 module load libGLU/9.0.3-cpeCray-23.03 module load HarfBuzz/8.2.2-cpeCray-23.03 export TOPAS_G4_DATA_DIR=$HOME/Applications/GEANT4/G4DATA export LD_LIBRARY_PATH=$HOME/Applications/TOPAS/OpenTOPAS-install/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=$HOME/Applications/GEANT4/geant4-install/lib:$LD_LIBRARY_PATH $HOME/Applications/TOPAS/OpenTOPAS-install/bin/topas $1 Eof chomd +x topas echo 'export PATH=~/Applications/shellScripts:$PATH' >> $HOME/.bashrc |
9. Run OpenTOPAS on LANTA
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Since OpenTOPAS does NOT installed with Qt, the option |
Two approaches for running OpenTOPAS on LANTA are presented below.
The second approach using
sinteractcommand can be useful. However, this method is not recommended if your internet connection is poor or you have to runtopasfor a long time.
A. Batch job
This first approach, using a job script and sbatch command, is
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recommended. For performance reasons, every graphic option, Gr/*/, should be disabled, please visit https://opentopas.readthedocs.io/en/latest/parameters/graphics.html for complete details.
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Essentially, please check that |
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be paused on the system until time out, wasting your SHr! |
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The second approach using sinteract command can be useful. However, this method is not recommended if your internet connection is poor or you have to run topas for a long time.
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Below is a template of OpenTOPAS job script. It can be created using vi submitTOPAS.sh. Edit it to meet your demands.
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#!/bin/bash
#SBATCH -p compute # Partition
#SBATCH -N 1 # Number of node
#SBATCH --ntasks-per-node=1 # Number of MPI processes per node
#SBATCH --cpus-per-task=16 # Number of OpenMP threads per MPI process
#SBATCH -t 120:00:00 # Job runtime limit
#SBATCH -J TOPAS # Job name
#SBATCH -A ltxxxxxx # Account *** {USER EDIT} ***
source $HOME/.bashrc
echo "Use topas = $(which topas)"
topas xxx.txt # Your case *** {USER EDIT} *** | ||
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In your case file, b:Ts/PauseBeforeQuit MUST set to "False", otherwise your job will run indefinitely until time out. |
To submit this job script to the SLURM queuing system, execute
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(Also see https://thaisc.atlassian.net/wiki/spaces/LANTA/pages/447021064/Quick+Start+Guide#6.-Running-your-job)
B. Interactive session
You can directly access LANTA computing nodes by requesting an interactive session. For example, execute
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(You could add -X option to enable X11 forwarding for OpenGL-related features such as CopyOpenGLToSVG/graphic features. Please visit Interactive session and https://opentopas.readthedocs.io/en/latest/parameters/graphics.html before using this capability)
After the requested resources are allocated, you can use this session to run topas and interactively execute Geant4 commands afterwards. For example,
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topas $HOME/Applications/TOPAS/OpenTOPAS-install/examples/Basic/TwoBeams.txt |
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