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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 -Lwget https://github.com/indigo-dc/udocker/releases/download/v11.3.4/udocker-1.3.4.tar.gz > udocker-1.3.4.tar.gz tar zxvf udocker-1.3.4.tar.gz > ~/.local/bin/udocker-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${WORK}/udocker/udocker create --name=imas imas/fc2k ~/.local/bin/${WORK}/udocker/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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