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Updated: 15 September 2024

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.)

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]

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]

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

  • -DCMAKE_PREFIX_PATH=/usr/lib/qt5 -DGEANT4_USE_QT=ON is changed to -DGEANT4_USE_QT=OFF.

  • /geant4-install/lib is symbolically linked to /geant4-install/lib64.

4. Download G4DATA [Step 6]

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 /project/common/G4DATA. 

cd $HOME/Applications/GEANT4/
cp -r /project/common/G4DATA .

5. Download OpenTOPAS [Step 8.1]

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.

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]

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]

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

Since OpenTOPAS does NOT installed with Qt, b:Ts/UseQt = "False" must always be used.

Two approaches for running OpenTOPAS on LANTA are presented below.

  • The first approach using sbatch command is generally recommended. However, users MUST ensure that b:Ts/PauseBeforeQuit is set to "False", otherwise your job will run on the system until time out, wasting your SHr!

  • 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.

A. Job submission script

Below is a template of OpenTOPAS job script. It can be created using vi submitTOPAS.sh. Edit it to meet your demands.

#!/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} ***

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

sbatch submitTOPAS.sh

(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 

sinteract -p compute -c 16 -t 06:00:00

(You could add -X option to enable X11 forwarding for OpenGL-related features such as CopyOpenGLToSVG. Please visit Interactive session 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,

topas $HOME/Applications/TOPAS/OpenTOPAS-install/examples/Basic/TwoBeams.txt

Contact Us
ThaiSC support service : thaisc-support@nstda.or.th

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