source: flex_extract.git/For_developers/Sphinx/source/Documentation/Input/templates.rst @ b1674ed

*********
Templates
*********

In ``flex_extract`` we use the Python package `genshi <https://genshi.edgewall.org/>`_ to create specific files from templates. It is the most efficient way to be able to quickly adapt e.g. the job scripts send to the ECMWF batch queue system or the namelist file für the Fortran program without the need to change the program code. 

.. note::
   Usually it is not recommended to change anything in these files without being able to understand the effects.
   
Each template file has its content framework and keeps so-called placeholder variables in the positions where the values needs to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Kornshell job scripts, where (environment) variables are used the ``$`` sign needs to be doubled to `escape` and keep a single ``$`` sign as it is.
   
The following templates are used and can be found in directory ``flex_extract_vX.X/Templates``:

convert.nl
----------

    This is the template for a Fortran namelist file called ``fort.4`` which will be read by ``calc_etadot``.
    It contains all the parameters ``calc_etadot`` needs. 
    
    .. code-block:: fortran
 
        &NAMGEN
          maxl = $maxl,
          maxb = $maxb,
          mlevel = $mlevel,
          mlevelist = "$mlevelist",
          mnauf = $mnauf,
          metapar = $metapar,
          rlo0 = $rlo0,
          rlo1 = $rlo1,
          rla0 = $rla0,
          rla1 = $rla1,
          momega = $momega,
          momegadiff = $momegadiff,
          mgauss = $mgauss,
          msmooth = $msmooth,
          meta = $meta,
          metadiff = $metadiff,
          mdpdeta = $mdpdeta
        /

ecmwf_env.template
------------------

    This template is used to create the ``ECMWF_ENV`` file in the application modes **gateway** and **remote**. It contains the user credentials and gateway server settings for the file transfers.

    .. code-block:: bash
    
        ECUID $user_name
        ECGID $user_group
        GATEWAY $gateway_name
        DESTINATION $destination_name

compilejob.template
-------------------

    This template is used to create the job script file called ``compilejob.ksh`` during the installation process for the application modes **remote** and **gateway**. 

    At the beginning some directives for the batch system are set. 
    On the **ecgate** server the ``SBATCH`` comments are the directives for the SLURM workload manager. A description of the single lines can be found at `SLURM directives <https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs>`_.
    For the high performance computers **cca** and **ccb** the ``PBS`` comments are necessary and can be view at `PBS directives <https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS>`_.

    The software environment requirements mentioned in :ref:`ref-requirements` are prepared by loading the corresponding modules depending in the ``HOST``. It should not be changed without testing.
    
    Afterwards the installation steps as such are done. Including the generation of the root directory, putting files in place, compiling the Fortran program and sending a log file via email.

    .. code-block:: ksh
    
        #!/bin/ksh

        # ON ECGB:
        # start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE  on gateway server
        # start with sbatch NAME_OF_THIS_FILE directly on machine

        #SBATCH --workdir=/scratch/ms/$usergroup/$username
        #SBATCH --qos=normal
        #SBATCH --job-name=flex_ecmwf
        #SBATCH --output=flex_ecmwf.%j.out
        #SBATCH --error=flex_ecmwf.%j.out
        #SBATCH --mail-type=FAIL
        #SBATCH --time=12:00:00

        ## CRAY specific batch requests
        ##PBS -N flex_ecmwf
        ##PBS -q ns
        ##PBS -S /usr/bin/ksh
        ##PBS -o /scratch/ms/$usergroup/$username/flex_ecmwf.$${Jobname}.$${Job_ID}.out
        # job output is in .ecaccess_DO_NOT_REMOVE
        ##PBS -j oe
        ##PBS -V
        ##PBS -l EC_threads_per_task=1
        ##PBS -l EC_memory_per_task=3200MB

        set -x
        export VERSION=$version_number
        case $${HOST} in
          *ecg*)
          module unload grib_api
          module unload eccodes
          module unload python
          module unload emos
          module load python3
          module load eccodes/2.12.0
          module load emos/455-r64
          export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
          export MAKEFILE=$makefile
          ;;
          *cca*)
          module unload python
          module switch PrgEnv-cray PrgEnv-intel
          module load python3
          module load eccodes/2.12.0
          module load emos
          echo $${GROUP}
          echo $${HOME}
          echo $${HOME} | awk -F / '{print $1, $2, $3, $4}'
          export GROUP=`echo $${HOME} | awk -F / '{print $4}'`
          export SCRATCH=/scratch/ms/$${GROUP}/$${USER}
          export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
          export MAKEFILE=$makefile
          ;;
        esac

        mkdir -p $${FLEXPART_ROOT_SCRIPTS}/flex_extract_v$${VERSION}
        cd $${FLEXPART_ROOT_SCRIPTS}/flex_extract_v$${VERSION}   # if FLEXPART_ROOT is not set this means cd to the home directory
        tar -xvf $${HOME}/flex_extract_v$${VERSION}.tar
        cd Source/Fortran
        \rm *.o *.mod $fortran_program 
        make -f $${MAKEFILE} >flexcompile 2>flexcompile

        ls -l $fortran_program >>flexcompile
        if [ $$? -eq 0 ]; then
          echo 'SUCCESS!' >>flexcompile
          mail -s flexcompile.$${HOST}.$$$$ $${USER} <flexcompile
        else
          echo Environment: >>flexcompile
          env >> flexcompile
          mail -s "ERROR! flexcompile.$${HOST}.$$$$" $${USER} <flexcompile
        fi


job.temp
--------

    This template is used to create the actual job script file called ``job.ksh`` for the execution of ``flex_extract`` in the application modes **remote** and **gateway**. 

    At the beginning some directives for the batch system are set. 
    On the **ecgate** server the ``SBATCH`` comments are the directives for the SLURM workload manager. A description of the single lines can be found at `SLURM directives <https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs>`_.
    For the high performance computers **cca** and **ccb** the ``PBS`` comments are necessary and can be view at `PBS directives <https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS>`_.

    The software environment requirements mentioned in :ref:`ref-requirements` are prepared by loading the corresponding modules depending in the ``HOST``. It should not be changed without testing.
    
    Afterwards the run directory and the ``CONTROL`` file are created and ``flex_extract`` is executed. In the end a log file is send via email.
    
    .. code-block:: ksh
    
        #!/bin/ksh

        # ON ECGB:
        # start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE  on gateway server
        # start with sbatch NAME_OF_THIS_FILE directly on machine

        #SBATCH --workdir=/scratch/ms/at/km4a
        #SBATCH --qos=normal
        #SBATCH --job-name=flex_ecmwf
        #SBATCH --output=flex_ecmwf.%j.out
        #SBATCH --error=flex_ecmwf.%j.out
        #SBATCH --mail-type=FAIL
        #SBATCH --time=12:00:00

        ## CRAY specific batch requests
        ##PBS -N flex_ecmwf
        ##PBS -q np
        ##PBS -S /usr/bin/ksh
        ## -o /scratch/ms/at/km4a/flex_ecmwf.$${PBS_JOBID}.out
        ## job output is in .ecaccess_DO_NOT_REMOVE
        ##PBS -j oe
        ##PBS -V
        ##PBS -l EC_threads_per_task=24
        ##PBS -l EC_memory_per_task=32000MB

        set -x
        export VERSION=7.1
        case $${HOST} in
          *ecg*)
          module unload grib_api
          module unload eccodes
          module unload python
          module unload emos
          module load python3
          module load eccodes/2.12.0
          module load emos/455-r64
          export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
          ;;
          *cca*)
          module unload python
          module switch PrgEnv-cray PrgEnv-intel
          module load python3
          module load eccodes/2.12.0
          module load emos
          export SCRATCH=$${TMPDIR}
          export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
          ;;
        esac

        cd $${SCRATCH}
        mkdir -p python$$$$
        cd python$$$$

        export CONTROL=CONTROL

        cat >$${CONTROL}<<EOF
        $control_content
        EOF


        submit.py --controlfile=$${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1

        if [ $? -eq 0 ] ; then
          l=0
          for muser in `grep -i MAILOPS $${CONTROL}`; do
              if [ $${l} -gt 0 ] ; then 
                 mail -s flex.$${HOST}.$$$$ $${muser} <prot
              fi
              l=$(($${l}+1))
          done
        else
          l=0
          for muser in `grep -i MAILFAIL $${CONTROL}`; do
              if [ $${l} -gt 0 ] ; then 
                 mail -s "ERROR! flex.$${HOST}.$$$$" $${muser} <prot
              fi
              l=$(($${l}+1))
          done
        fi
        

job.template
------------

    This template is used to create the template for the execution job script ``job.temp`` for ``flex_extract`` in the installation process. A description of the file can be found under ``job.temp``. A couple of parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
        
    .. code-block:: ksh
    
        #!/bin/ksh

        # ON ECGB:
        # start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE  on gateway server
        # start with sbatch NAME_OF_THIS_FILE directly on machine

        #SBATCH --workdir=/scratch/ms/$usergroup/$username
        #SBATCH --qos=normal
        #SBATCH --job-name=flex_ecmwf
        #SBATCH --output=flex_ecmwf.%j.out
        #SBATCH --error=flex_ecmwf.%j.out
        #SBATCH --mail-type=FAIL
        #SBATCH --time=12:00:00

        ## CRAY specific batch requests
        ##PBS -N flex_ecmwf
        ##PBS -q np
        ##PBS -S /usr/bin/ksh
        ## -o /scratch/ms/$usergroup/$username/flex_ecmwf.$$$${PBS_JOBID}.out
        ## job output is in .ecaccess_DO_NOT_REMOVE
        ##PBS -j oe
        ##PBS -V
        ##PBS -l EC_threads_per_task=24
        ##PBS -l EC_memory_per_task=32000MB

        set -x
        export VERSION=$version_number
        case $$$${HOST} in
          *ecg*)
          module unload grib_api
          module unload eccodes
          module unload python
          module unload emos
          module load python3
          module load eccodes/2.12.0
          module load emos/455-r64
          export PATH=$$$${PATH}:$fp_root_path
          ;;
          *cca*)
          module unload python
          module switch PrgEnv-cray PrgEnv-intel
          module load python3
          module load eccodes/2.12.0
          module load emos
          export SCRATCH=$$$${TMPDIR}
          export PATH=$$$${PATH}:$fp_root_path
          ;;
        esac

        cd $$$${SCRATCH}
        mkdir -p python$$$$$$$$
        cd python$$$$$$$$

        export CONTROL=CONTROL

        cat >$$$${CONTROL}<<EOF
        $$control_content
        EOF


        submit.py --controlfile=$$$${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1

        if [ $? -eq 0 ] ; then
          l=0
          for muser in `grep -i MAILOPS $$$${CONTROL}`; do
              if [ $$$${l} -gt 0 ] ; then 
                 mail -s flex.$$$${HOST}.$$$$$$$$ $$$${muser} <prot
              fi
              l=$(($$$${l}+1))
          done
        else
          l=0
          for muser in `grep -i MAILFAIL $$$${CONTROL}`; do
              if [ $$$${l} -gt 0 ] ; then 
                 mail -s "ERROR! flex.$$$${HOST}.$$$$$$$$" $$$${muser} <prot
              fi
              l=$(($$$${l}+1))
          done
        fi







  





   
   

 
   
   

.. toctree::
    :hidden:
    :maxdepth: 2