Changeset b1674ed in flex_extract.git for For_developers/Sphinx/source/Documentation/Input


Ignore:
Timestamp:
Apr 1, 2020, 5:03:13 PM (4 years ago)
Author:
Anne Philipp <anne.philipp@…>
Branches:
master, ctbto, dev
Children:
d78851d, e0005c9
Parents:
50f9ca6
Message:

updated online documentation FIX for tickets #265 and #262

Location:
For_developers/Sphinx/source/Documentation/Input
Files:
10 edited

Legend:

Unmodified
Added
Removed

  • For_developers/Sphinx/source/Documentation/Input/compilejob.rst

    rba99230 rb1674ed  
    7474      module load emos/455-r64
    7575      export FLEXPART_ROOT_SCRIPTS=${HOME}
    76       export MAKEFILE=Makefile.gfortran
     76      export MAKEFILE=makefile_ecgate
    7777      ;;
    7878      *cca*)
    … …  
    8888      export SCRATCH=/scratch/ms/${GROUP}/${USER}
    8989      export FLEXPART_ROOT_SCRIPTS=${HOME}
    90       export MAKEFILE=Makefile.gfortran
     90      export MAKEFILE=makefile_ecgate
    9191      ;;
    9292    esac
    … …  
    9595    cd ${FLEXPART_ROOT_SCRIPTS}/flex_extract_v${VERSION}   # if FLEXPART_ROOT is not set this means cd to the home directory
    9696    tar -xvf ${HOME}/flex_extract_v${VERSION}.tar
    97     cd source/fortran
    98     \rm *.o *.mod CONVERT2
     97    cd Source/Fortran
     98    \rm *.o *.mod calc_etadot
    9999    make -f ${MAKEFILE} >flexcompile 2>flexcompile
    100100
    101     ls -l CONVERT2 >>flexcompile
     101    ls -l calc_etadot >>flexcompile
    102102    if [ $? -eq 0 ]; then
    103103      echo 'SUCCESS!' >>flexcompile

  • For_developers/Sphinx/source/Documentation/Input/control.rst

    rd9abaac rb1674ed  
    3434--------------------------------
    3535
    36 A number of example files can be found in the directory :literal:`flex_extract_vX.X/run/control/`.
     36A number of example files can be found in the directory :literal:`flex_extract_vX.X/Run/Control/`.
    3737They can be used as a template for adaptations and understand what's possible to
    3838retrieve from ECMWF's archive.

  • For_developers/Sphinx/source/Documentation/Input/control_params.rst

    rba99230 rb1674ed  
    44     
    55   
     6
    67   
    78.. _ref-control-user:

  • For_developers/Sphinx/source/Documentation/Input/ecmwf_env.rst

    r30f7911 rb1674ed  
    33****************************************
    44
    5 This file contains the user credentials for working on ECMWF servers and transferring files between the ECMWF servers and the local gateway server. It is located in the ``flex_extract_vX.X/run`` directory and will be created in the installation process for the application modes **remote** and **gateway**.
     5This file contains the user credentials for working on ECMWF servers and transferring files between the ECMWF servers and the local gateway server. It is located in the ``flex_extract_vX.X/Run`` directory and will be created in the installation process for the application modes **remote** and **gateway**.
    66
    77This file is based on the template ``ECMWF_ENV.template`` which is located in the ``templates`` directory.
    … …  
    99.. note::
    1010 
    11    In the **local** mode it is not present.
     11   In the **local** mode this file is not present.
    1212
    1313

  • For_developers/Sphinx/source/Documentation/Input/examples.rst

    rba99230 rb1674ed  
    33**********************
    44
    5 ``Flex_extract`` has a couple of example ``CONTROL`` files for a number of different data set constellations in the directory path ``flex_extract_vX.X/run/control``.
     5``Flex_extract`` has a couple of example ``CONTROL`` files for a number of different data set constellations in the directory path ``flex_extract_vX.X/Run/Control``.
    66
    77Here is a list of the example files and a description of the data set:
    … …  
    1010   This file is not intended to be used with ``flex_extract``. It has a list of all possible parameters and their default values for a quick overview.
    1111   
    12 CONTROL_CERA
    13 CONTROL_CERA.global
    14 CONTROL_CERA.public
    15 CONTROL_EA5
    16 CONTROL_EA5.global
    17 CONTROL_EA5.public
    18 CONTROL_EI
    19 CONTROL_EI.global
    20 CONTROL_EI.public
    21 CONTROL_OD.ELDA.FC.eta.ens.double
    22 CONTROL_OD.ENFO.CF
    23 CONTROL_OD.ENFO.CV
    24 CONTROL_OD.ENFO.PF
    25 CONTROL_OD.ENFO.PF.36hours
    26 CONTROL_OD.ENFO.PF.ens
    27 CONTROL_OD.OPER.4V.operational
    28 CONTROL_OD.OPER.FC.36hours
    29 CONTROL_OD.OPER.FC.eta.global
    30 CONTROL_OD.OPER.FC.eta.highres
    31 CONTROL_OD.OPER.FC.gauss.highres
    32 CONTROL_OD.OPER.FC.operational
    33 CONTROL_OD.OPER.FC.twiceaday.1hourly
    34 CONTROL_OD.OPER.FC.twiceaday.3hourly
     12.. code-block:: bash
     13
     14        CONTROL_CERA
     15        CONTROL_CERA.global
     16        CONTROL_CERA.public
     17        CONTROL_EA5
     18        CONTROL_EA5.global
     19        CONTROL_EA5.public
     20        CONTROL_EI
     21        CONTROL_EI.global
     22        CONTROL_EI.public
     23        CONTROL_OD.ELDA.FC.eta.ens.double
     24        CONTROL_OD.ENFO.CF
     25        CONTROL_OD.ENFO.CV
     26        CONTROL_OD.ENFO.PF
     27        CONTROL_OD.ENFO.PF.36hours
     28        CONTROL_OD.ENFO.PF.ens
     29        CONTROL_OD.OPER.4V.operational
     30        CONTROL_OD.OPER.FC.36hours
     31        CONTROL_OD.OPER.FC.eta.global
     32        CONTROL_OD.OPER.FC.eta.highres
     33        CONTROL_OD.OPER.FC.gauss.highres
     34        CONTROL_OD.OPER.FC.operational
     35        CONTROL_OD.OPER.FC.twiceaday.1hourly
     36        CONTROL_OD.OPER.FC.twiceaday.3hourly
    3537
    3638   

  • For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst

    rba99230 rb1674ed  
    1 ***********************************
    2 The Fortran Makefile - ``CONVERT2``
    3 ***********************************
     1**************************************
     2The Fortran Makefile - ``calc_etadot``
     3**************************************
    44
    55.. _ref-convert:
    66
    77``Flex_extract``'s Fortran program will be compiled during
    8 the installation process to get the executable named ``CONVERT2``.
     8the installation process to get the executable named ``calc_etadot``.
    99
    10 ``flex_extract`` has a couple of ``Makefiles`` prepared which can be found in the directory
    11 ``flex_extract_vX.X/source/fortran``, where ``vX.X`` should be substituted with the current version number.
    12 A list of these ``Makefiles`` are shown below:
     10``Flex_extract`` has a couple of ``makefiles`` prepared which can be found in the directory
     11``flex_extract_vX.X/Source/Fortran``, where ``vX.X`` should be substituted with the current version number.
     12A list of these ``makefiles`` are shown below:
    1313
    1414
    … …  
    1616| Files to be used as they are!
    1717   
    18     | **Makefile.gfortran**
     18    | **makefile_ecgate**
    1919    | For the use on ECMWF's server **ecgate**.
    2020
    21     | **Makefile.CRAY**
     21    | **makefile_cray**
    2222    | For the use on ECMWF's server **cca/ccb**.
    2323   
    … …  
    2525| It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB**
    2626 
    27     | **Makefile.local.gfortran**
    28     | For the use with gfortran compiler.
     27    | **makefile_fast**
     28    | For the use with gfortran compiler and optimization mode.
    2929
    30     | **Makefile.local.ifort**
    31     | For the use with ifort compiler.
     30    | **makefile_debug**
     31    | For the use with gfortran compiler in debugging mode.
    3232
    3333
    34 For instructions on how to adapt the ``Makefiles`` for the local application mode
     34For instructions on how to adapt the ``makefiles`` for the local application mode
    3535please see :ref:`ref-install-local`.
    3636

  • For_developers/Sphinx/source/Documentation/Input/jobscript.rst

    rba99230 rb1674ed  
    55The jobscript 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 which is stored in the ``templates`` directory.
    8 This template is by itself generated in the installation process from a ``jobscript.template`` template file.
     7It is based on the ``job.temp`` template file which is stored in the ``Templates`` directory.
     8This template is by itself generated in the installation process from a ``job.template`` template file.
    99
    1010``Flex_extract`` uses the python package `genshi <https://genshi.edgewall.org/>`_ to generate
    … …  
    7474      module load eccodes/2.12.0
    7575      module load emos/455-r64
    76       export PATH=${PATH}:${HOME}/flex_extract_v7.1/source/python
     76      export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
    7777      ;;
    7878      *cca*)
    … …  
    8383      module load emos
    8484      export SCRATCH=${TMPDIR}
    85       export PATH=${PATH}:${HOME}/flex_extract_v7.1/source/python
     85      export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
    8686      ;;
    8787    esac

  • For_developers/Sphinx/source/Documentation/Input/run.rst

    rba99230 rb1674ed  
    1111Based on these input information ``flex_extract`` applies one of the application modes to either retrieve the ECMWF data via a Web API on a local maschine or submit a jobscript to ECMWF servers and retrieve the data there with sending the files to the local system eventually.
    1212
    13 
    14 
    15 PUT IN HERE A BLOCKDIAGRAM OF RAW PROGRAM FLOW
    1613
    1714
    … …  
    4340
    4441It is also possible to start ``flex_extract`` directly from command line by using the ``submit.py`` script instead of the wrapping Shell script ``run.sh``.  This top-level script is located in
    45 ``flex_extract_vX.X/source/python`` and is executable. With the ``help`` parameter we see again all possible
     42``flex_extract_vX.X/Source/Python`` and is executable. With the ``help`` parameter we see again all possible
    4643command line parameter.
    4744

  • For_developers/Sphinx/source/Documentation/Input/setup.rst

    rba99230 rb1674ed  
    1313- copying tar-ball to target location (depending on application mode and installation path)
    1414- submit compilation script to batch queue at ECMWF servers (in **remote** and **gateway** mode) or just untar tar-ball at target location (**local mode**)
    15 - compilation of the FORTRAN90 program ``CONVERT2``
     15- compilation of the FORTRAN90 program ``calc_etadot``
    1616
    1717
    … …  
    156156
    157157It is also possible to start the installation process of ``flex_extract`` directly from command line by using the ``install.py`` script instead of the wrapping Shell script ``setup.sh``.  This top-level script is located in
    158 ``flex_extract_vX.X/source/python`` and is executable. With the ``help`` parameter we see again all possible
     158``flex_extract_vX.X/Source/Python`` and is executable. With the ``help`` parameter we see again all possible
    159159command line parameter.
    160160

  • For_developers/Sphinx/source/Documentation/Input/templates.rst

    rba99230 rb1674ed  
    33*********
    44
    5 In ``flex_extract`` we use the Python package ``genshi`` (`ref <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.
     5In ``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.
    66
    77.. note::
    … …  
    1515----------
    1616
    17     This is the template for a Fortran namelist file called ``fort.4`` which will be read by ``CONVERT2``.
    18     It contains all the parameters ``CONVERT2`` needs.
     17    This is the template for a Fortran namelist file called ``fort.4`` which will be read by ``calc_etadot``.
     18    It contains all the parameters ``calc_etadot`` needs.
    1919   
    2020    .. code-block:: fortran
    … …  
    125125        cd $${FLEXPART_ROOT_SCRIPTS}/flex_extract_v$${VERSION}   # if FLEXPART_ROOT is not set this means cd to the home directory
    126126        tar -xvf $${HOME}/flex_extract_v$${VERSION}.tar
    127         cd source/fortran
     127        cd Source/Fortran
    128128        \rm *.o *.mod $fortran_program
    129129        make -f $${MAKEFILE} >flexcompile 2>flexcompile
    … …  
    191191          module load eccodes/2.12.0
    192192          module load emos/455-r64
    193           export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/source/python
     193          export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
    194194          ;;
    195195          *cca*)
    … …  
    200200          module load emos
    201201          export SCRATCH=$${TMPDIR}
    202           export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/source/python
     202          export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
    203203          ;;
    204204        esac
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