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Latest IMAS Docker image

• IMAS version: 3.2328.1
• UAL version: 4.08.31
• Kepler version: 2.5p4-develop5p5-3.2.0
• FC2K version: 4.611.0
• Available on the EF Gateway: ~g2tomz/public/imas-fc2k-3latest.23.1-4.0.3-2.5p4-develop-4.6.0tar.xz
• Available on the ITER node hpc-login02.iter.org: ~zokt/public/imas-fc2k-latest.tar.xz

Important

1. Below you will find instructions with example commands to run.
2. Commands to be run on your local machine will be marked with red color.
3. Commands to be run on the Gateway will be marked with green color.
4. Commands to be run in the running container will be marked with blue color.  
5. The documentation covers usage of both Docker (running on your own computer) and uDocker (running on the Gateway). You do not have to follow both scenarios.

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• Docker on your own computer:
  • Follow instructions at Docker for Windows, or
  • Follow instructions at Docker for Mac, or
  • Follow instructions at Docker for CentOS, Docker for Debian, Docker for Fedora or Docker for Ubuntu

• uDocker:

  Code Block
  language bash
  if grep MARCONI /etc/motd &>/dev/null; then WORK=${WORK} SCRATCH=${CINECA_SCRATCH} stat ${WORK} &>/dev/null || WORK=${HOME}/work elif grep 'Nord III' /etc/motd &>/dev/null; then WORK=/gpfs/projects/$(id -gn)/$(id -un) SCRATCH=/gpfs/scratch/$(id -gn)/$(id -un) else WORK=${HOME}/work SCRATCH=${HOME}/scratch fi   mkdir -p ~/.local/bin ${WORK}/dot-udocker ${SCRATCH} ln -s ${WORK}/dot-udocker ~/.udocker curl wget https://raw.githubusercontentgithub.com/indigo-dc/udocker/master/udocker.py > ~/.local/bin/udocker/releases/download/1.3.4/udocker-1.3.4.tar.gz tar zxvf udocker-1.3.4.tar.gz -C ${WORK}/ chmod u+rx ~/.local/bin${WORK}/udocker echo "tmpdir='${SCRATCH}'" > ~/.udocker/udocker.conf ~/.local/bin #test udocker exec ${WORK}/udocker/udocker --help #install ${WORK}/udocker/udocker install

  
  

  Info
  title uDocker startup errors
  If ${WORK}/udocker/udocker  command throws errors try to add python3  command before path. Code Block module load itm-python/3.10 python3 ${WORK}/udocker/udocker --help python3 ${WORK}/udocker/udocker install

  
  

Loading Docker image

• Docker on your own computer:

  Code Block
  language bash
  # Linux scp login.eufus.eu:~g2tomz/public/imas-fc2k-latest.tar.xz ./ xzcat imas-fc2k-latest.tar.xz | docker load # macOS scp login.eufus.eu:~g2tomz/public/imas-fc2k-latest.tar.xz ./ docker load < imas-fc2k-latest.tar.xz

  
  

• uDocker on Gateway:

  Code Block
  language bash
  ~/.local/bin/${WORK}/udocker/udocker load -i ~g2tomz/public/imas-fc2k-latest.tar.xz

  
  

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• Create a container and start a shell in it:

  • Docker on your own computer:

    Code Block
    language bash
    docker run --interactive --tty --name imas imas/fc2k

    
    

  • uDocker on Gateway:

    Code Block
    language bash
    export PROOT_NO_SECCOMP=1 ~/.local/bin${WORK}/udocker/udocker create --name=imas imas/fc2k ~/.local/bin/${WORK}/udocker/udocker run imas

    
    

• In the container shell, execute:

  Code Block
  language bash
  cat << EOF > put_pf.py   import imas if __name__ == '__main__': ids = imas.ids(1, 1, 1, 1) ids.create_env('imas', 'test', '3') ids.pf_active.ids_properties.comment = 'Test data' ids.pf_active.ids_properties.homogeneous_time = 0 ids.pf_active.coil.resize(2) ids.pf_active.coil[0].name = 'COIL 1A' ids.pf_active.coil[1].name = 'COIL 2B' number = 10 ids.pf_active.coil[0].current.data.resize(number) ids.pf_active.coil[0].current.time.resize(number) for i in range(number): ids.pf_active.coil[0].current.data[i] = 2 * i ids.pf_active.coil[0].current.time[i] = i number = number + 2 ids.pf_active.coil[1].current.data.resize(number) ids.pf_active.coil[1].current.time.resize(number) for i in range(number): ids.pf_active.coil[1].current.data[i] = 2 * i + 10 ids.pf_active.coil[1].current.time[i] = i + number ids.pf_active.put() EOF   python put_pf.py

  
  

• Transfer the results to the Gateway:

  • Docker on your own computer:

    Code Block
    language bash
    docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.characteristics /tmp/ docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.datafile /tmp/ docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.tree /tmp/ scp /tmp/ids_10001.* login.eufus.eu:public/imasdb/test/3/0/

    
    

  • uDocker on Gateway:

    Code Block
    language bash
    cp ~${WORK}/.udocker/containers/imas/ROOT/home/imas/public/imasdb/test/3/0/ids_10001.* ~/public/imasdb/test/3/0/

    
    

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• Create a container and start a shell in it:

  • Docker on your own computer:

    Code Block
    language bash
    docker run --interactive --tty --name imas imas/fc2k

    
    

  • uDocker on Gateway:

    Code Block
    language bash
    ~/.local/bin${WORK}/udocker/udocker create --name=imas imas/fc2k ~/.local/bin/udocker run --user root imas pip install 'matplotlib<3' ~/.local/bin${WORK}/udocker/udocker run --user root imas pip3 install 'matplotlib<3.1' ~/.local/bin/udocker run --user root imas apt-get install -y python-tk python3-tk ~/.local/bin/udocker run imas

    
    

• Transfer the Kepler workflow into the container

  • Docker on your own computer:

    Code Block
    scp login.eufus.eu:~g2tomz/public/simple-workflow.xml ./ docker cp simple-workflow.xml imas:simple-workflow.xml

    
    

  • uDocker on Gateway:

    Code Block
    cp ~g2tomz/public/simple-workflow.xml ~/.udocker/containers/imas/ROOT/home/imas/

    
    

• In the container shell, execute:

  Code Block
  language bash
  cp $IMAS_PREFIX/models/mdsplus/ids_model.characteristics public/imasdb/test/3/0/ids_19998.characteristics cp $IMAS_PREFIX/models/mdsplus/ids_model.datafile public/imasdb/test/3/0/ids_19998.datafile cp $IMAS_PREFIX/models/mdsplus/ids_model.tree public/imasdb/test/3/0/ids_19998.tree kepler -runwf -nogui -user imas /home/imas/simple-workflow.xml

  
  

• Transfer the results to the Gateway:

  • Docker on your own computer:

    Code Block
    language bash
    docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.characteristics /tmp/ docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.datafile /tmp/ docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.tree /tmp/ scp /tmp/ids_10001.* login.eufus.eu:public/imasdb/test/3/0/

    
    

  • uDocker on Gateway:

    Code Block
    language bash
    cp ~${WORK}/.udocker/containers/imas/ROOT/home/imas/public/imasdb/test/3/0/ids_10001.* ~/public/imasdb/test/3/0/

    
    

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