Changeset 6931f61 in flex_extract.git for Documentation/html/_sources/Documentation


Ignore:
Timestamp:
Jul 8, 2020, 10:00:37 PM (4 years ago)
Author:
anphi <anne.philipp@…>
Branches:
master, ctbto, dev
Children:
e0005c9
Parents:
8a53342
Message:

Update Onlinedocumentation after review of language editing

Location:
Documentation/html/_sources/Documentation
Files:
9 edited

Legend:

Unmodified
Added
Removed

  • Documentation/html/_sources/Documentation/Input/compilejob.rst.txt

    r5920b7f r6931f61  
    1 *********************************************
     1*************************************************
    22The compilation job script ``compilejob.ksh``
    3 *********************************************
     3*************************************************
    44
    5 The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.
     5The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``installscript.template`` in the template directory.
    66
    77``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
    88the Korn-shell script from the template files by substituting the individual parameters.
    9 These individual parameters are marked by a doubled ``$`` sign in ``job.temp``.
     9These individual parameters are marked by a doubled ``$`` sign in ``installscript.template``.
    1010
    11 The job script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
     11The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
    1212server system to load the necessary modules for the environment when submitted to the batch queue.
    1313
    … …  
    2424 #. It creates the ``flex_extract`` root directory in the ``$HOME`` path of the user
    2525 #. It untars the tarball into the root directory.
    26  #. It compiles the Fortran program using ``Makefile``.
     26 #. It compiles the Fortran program using ``makefile``.
    2727 #. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
    2828
    … …  
    6767      *ecg*)
    6868      module unload grib_api
    69       module unload eccodes
    70       module unload python
    7169      module unload emos
    7270      module load python3
    73       module load eccodes/2.12.0
     71      module load eccodes
    7472      module load emos/455-r64
    7573      export FLEXPART_ROOT_SCRIPTS=${HOME}
    … …  
    7775      ;;
    7876      *cca*)
    79       module unload python
    8077      module switch PrgEnv-cray PrgEnv-intel
    8178      module load python3
    82       module load eccodes/2.12.0
    83       module load emos
     79      module load eccodes
     80      module load emos/455-r64
    8481      echo ${GROUP}
    8582      echo ${HOME}

  • Documentation/html/_sources/Documentation/Input/examples.rst.txt

    r5920b7f r6931f61  
    3636        CONTROL_OD.OPER.FC.twicedaily.3hourly
    3737
    38 .. todo::
     38.. note::
    3939
    40    #PS some information to be added.
     40   Further information will follow.
    4141 
    4242.. toctree::

  • Documentation/html/_sources/Documentation/Input/jobscript.rst.txt

    r5bee29a r6931f61  
    55The job script is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
    66
    7 It is based on the ``job.temp`` template file stored in the ``Templates`` directory.
    8 This template is generated in the installation process from a ``job.template`` template file.
     7It is based on the ``submitscript.template`` template file stored in the ``Templates`` directory.
     8This template is generated in the installation process from a ``jobscript.template`` template file.
    99
    1010``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
    1111the Korn-shell script from the template files by substituting the individual parameters.
    12 These individual parameters are marked by ``$$`` in ``job.temp``.
     12These individual parameters are marked by ``$$`` in ``jobscript.template``.
    1313
    1414The job script has a number of settings for the batch system which are fixed, and differentiates between the *ecgate* and the *cca/ccb*
    … …  
    2626 #. It sets some environment variables for the single session.
    2727 #. It creates the directory structure in the user's ``$SCRATCH`` file system.
    28  #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``jobscript.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
     28 #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``job.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
    2929 #. ``Flex_extract`` is started from within the ``work`` directory of the new directory structure by calling the ``submit.py`` script. It sets new paths for input and output directories and the recently generated ``CONTROL`` file.
    3030 #. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
    … …  
    3333
    3434
    35 Example ``jobscript.ksh``
     35Example ``job.ksh``
    3636-------------------------
    3737 
    … …  
    6868      *ecg*)
    6969      module unload grib_api
    70       module unload eccodes
    71       module unload python
    7270      module unload emos
    7371      module load python3
    74       module load eccodes/2.12.0
     72      module load eccodes
    7573      module load emos/455-r64
    7674      export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
    7775      ;;
    7876      *cca*)
    79       module unload python
    8077      module switch PrgEnv-cray PrgEnv-intel
    8178      module load python3
    82       module load eccodes/2.12.0
    83       module load emos
     79      module load eccodes
     80      module load emos/455-r64
    8481      export SCRATCH=${TMPDIR}
    8582      export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
    … …  
    107104    date_chunk 3
    108105    debug 1
    109     destination annep@genericSftp
     106    destination <specificname>@genericSftp
    110107    doubleelda 0
    111108    dpdeta 1
    … …  
    128125    grib2flexpart 0
    129126    grid 1.0/1.0
    130     inputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
     127    inputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
    131128    install_target None
    132129    job_chunk 1
    … …  
    145142    omegadiff 0
    146143    oper 0
    147     outputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
     144    outputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
    148145    prefix CE
    149146    public 0

  • Documentation/html/_sources/Documentation/Input/run.rst.txt

    r5920b7f r6931f61  
    3131.. literalinclude:: ../../../../../Run/run.sh
    3232   :language: bash
    33    :caption: run.sh
    34 
     33   :caption:  run.sh
    3534
    3635

  • Documentation/html/_sources/Documentation/Input/templates.rst.txt

    r5920b7f r6931f61  
    88   Do not change anything in these files unless you understand the effects!
    99   
    10 Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need 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 for `escaping`.
     10Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Korn shell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
    1111   
    1212The following templates are used; they can be found in the directory ``flex_extract_vX.X/Templates``:
    1313
    14 convert.nl
    15 ----------
     14calc_etadot_nml.template
     15-------------------------
    1616
    1717    This is the template for a Fortran namelist file called ``fort.4`` read by ``calc_etadot``.
    … …  
    4040        /
    4141
    42 ecmwf_env.template
     42ECMWF_ENV.template
    4343------------------
    4444
    … …  
    5252        DESTINATION $destination_name
    5353
    54 compilejob.template
    55 -------------------
     54installscript.template
     55----------------------
    5656
    5757    This template is used to create the job script file called ``compilejob.ksh`` during the installation process for the application modes **remote** and **gateway**.
    … …  
    9797          *ecg*)
    9898          module unload grib_api
    99           module unload eccodes
    100           module unload python
    10199          module unload emos
    102100          module load python3
    103           module load eccodes/2.12.0
     101          module load eccodes
    104102          module load emos/455-r64
    105103          export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
    … …  
    107105          ;;
    108106          *cca*)
    109           module unload python
    110107          module switch PrgEnv-cray PrgEnv-intel
    111108          module load python3
    112           module load eccodes/2.12.0
    113           module load emos
     109          module load eccodes
     110          module load emos/455-r64
    114111          echo $${GROUP}
    115112          echo $${HOME}
    … …  
    140137
    141138
    142 job.temp
    143 --------
     139submitscript.template
     140---------------------
    144141
    145142    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**.
    … …  
    185182        case $${HOST} in
    186183          *ecg*)
    187           module unload grib_api
    188           module unload eccodes
    189           module unload python
    190           module unload emos
    191           module load python3
    192           module load eccodes/2.12.0
    193           module load emos/455-r64
    194           export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
    195           ;;
    196           *cca*)
    197           module unload python
    198           module switch PrgEnv-cray PrgEnv-intel
    199           module load python3
    200           module load eccodes/2.12.0
    201           module load emos
    202           export SCRATCH=$${TMPDIR}
    203           export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
     184                  module unload grib_api
     185                  module unload emos
     186                  module load python3
     187                  module load eccodes
     188                  module load emos/455-r64
     189                  export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
     190                  ;;
     191                  *cca*)
     192                  module switch PrgEnv-cray PrgEnv-intel
     193                  module load python3
     194                  module load eccodes
     195                  module load emos/455-r64
     196                  export SCRATCH=${TMPDIR}
     197                  export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
    204198          ;;
    205199        esac
    … …  
    237231       
    238232
    239 job.template
    240 ------------
    241 
    242     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``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
     233jobscript.template
     234------------------
     235
     236    This template is used to create the template for the execution job script ``submitscript.template`` for ``flex_extract`` in the installation process. A description of the file can be found under ``submitscript.template``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
    243237       
    244238    .. code-block:: ksh
    … …  
    273267        case $$$${HOST} in
    274268          *ecg*)
    275           module unload grib_api
    276           module unload eccodes
    277           module unload python
    278           module unload emos
    279           module load python3
    280           module load eccodes/2.12.0
    281           module load emos/455-r64
     269                  module unload grib_api
     270                  module unload emos
     271                  module load python3
     272                  module load eccodes
     273                  module load emos/455-r64
    282274          export PATH=$$$${PATH}:$fp_root_path
    283275          ;;
    284276          *cca*)
    285           module unload python
    286           module switch PrgEnv-cray PrgEnv-intel
    287           module load python3
    288           module load eccodes/2.12.0
    289           module load emos
     277                  module switch PrgEnv-cray PrgEnv-intel
     278                  module load python3
     279                  module load eccodes
     280                  module load emos/455-r64
    290281          export SCRATCH=$$$${TMPDIR}
    291282          export PATH=$$$${PATH}:$fp_root_path

  • Documentation/html/_sources/Documentation/disagg.rst.txt

    r5bee29a r6931f61  
    1313
    1414.. csv-table:: Flux fields
    15     :header: "Short Name", "Name", "Units", "Interpolation Type"
     15    :header: "Short Name", "Name", "Units", "Disaggregation"
    1616    :align: center
    1717    :widths: 5,15,5,10
    1818   
    19     LSP,  "large-scale precipitation",          "m",          "modified linear interpolation"
    20     CP,   "convective precipitation",           "m",          "modified linear interpolation"
    21     SSHF, "surface sensible heat flux",         "J m:math:`^{-2}`",   "bicubic interpolation"
    22     EWSS, "eastward turbulent surface stress",  "N m:math:`^{-2}` s", "bicubic interpolation"
    23     NSSS, "northward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
    24     SSR,  "surface net solar radiation",        "J m:math:`^{-2}`",   "bicubic interpolation"
     19    LSP,  "large-scale precipitation",          "m",          "precipitation "
     20    CP,   "convective precipitation",           "m",          "precipitation"
     21    SSHF, "surface sensible heat flux",         "J m :math:`^{-2}`",   "flux"
     22    EWSS, "eastward turbulent surface stress",  "N m :math:`^{-2}` s", "flux "
     23    NSSS, "northward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
     24    SSR,  "surface net solar radiation",        "J m :math:`^{-2}`",   "flux "
    2525   
    2626
    … …  
    4343
    4444In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in ``FLEXPART`` for all variables.
    45 This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
     45This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6).
    4646The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
    4747Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
    … …  
    161161     
    162162The accumulated values for the other variables are first divided by the number of hours and
    163 then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
    164 Disaggregation is done for four adjacent time intervals (:math:`p_a, p_b, p_c, p_d`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
     163then disaggregates to the exact times and conserves the integrals of the fluxes within each timespan.
     164Disaggregation is done for four adjacent time intervals (:math:`F_0, F_1, F_2, F_3`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
     165This new point :math:`F` is used for linear interpolation of the complete timeseries afterwards.
    165166
    166167.. math::
     168
    167169   
    168     p_a &= (a_3 - a_0 + 3. * (a_1 - a_2)) / 6. \\   
    169     p_b &= (a_2 + a_0) / 2. - a_1 - 9. * p_a / 2. \\
    170     p_c &= a_1 - a_0 - 7. * p_a / 2. - 2. * p_b \\   
    171     p_d &= a_0 - p_a / 4. - p_b / 3. - p_c / 2.
    172 
    173 This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards.
    174 
    175 .. math::
    176    
    177     p = 8. * p_a + 4. * p_b + 2. * p_c + p_d
     170    F = -\frac{1}{12}F_0 + \frac{7}{12}F_1 + \frac{7}{12}F_2 -\frac{1}{12}F_3
    178171
    179172

  • Documentation/html/_sources/Documentation/input.rst.txt

    r5920b7f r6931f61  
    3636       python3 Source/Python/submit.py --help
    3737   
    38     With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively.
    39     It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
     38   
     39    With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively. It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
    4040
    4141    ``flex_extract`` also creates the Korn shell scripts :doc:`Input/compilejob` and :doc:`Input/jobscript` which will be sent to the ECMWF servers in the **remote mode** and the **gateway mode** for starting batch jobs.

  • Documentation/html/_sources/Documentation/output.rst.txt

    r5920b7f r6931f61  
    8181
    8282
    83 Output files for pure forecast
     83Output files for long forecast
    8484------------------------------
    8585
    86 ``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:
     86``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in long forecast mode is introduced:
    8787
    8888.. code-block:: bash
    … …  
    194194
    195195
    196 VERTICAL.EC
    197 -----------
    198 
    199 This file contains information describing the vertical discretisation (model levels)
    200 in form of the ``A`` and ``B`` parameters which allow to calculate the actual pressure of a model level from the surface pressure.
    201 
    202196
    203197Index file
    … …  
    205199
    206200This file is called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
    207 
    208 .. todo::
    209 
    210         #PS NEEDS MORE DESCRIPTION
    211201
    212202

  • Documentation/html/_sources/Documentation/vertco.rst.txt

    r5920b7f r6931f61  
    77
    88Two methods are provided in ``flex_extract`` for the calculation of the vertical velocity for ``FLEXTRA``/``FLEXPART``:
    9     (i) from the horizontal wind field,
    10     (ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
     9
     10(i) from the horizontal wind field,
     11(ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
    1112
    1213Especially for high resolution data, use of the ``MARS`` parameter 77 is recommended,
    … …  
    3132    * For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (``RESOL=799``, ``SMOOTH=0``). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (``GAUSS=1``) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279  needs to be performed on *ecgate*, the computation of the vertical velocity is feasible only on the lat/lon grid (``GAUSS=0``), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.
    3233    * For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:
     34   
    3335        - For 1.0 degree grids: ``GAUSS=1``, ``RESOL=255``, ``SMOOTH=179``
    3436        - For 0.5 degree grids: ``GAUSS=1``, ``RESOL=399``, ``SMOOTH=359``
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