Changeset a14839a in flex_extract.git
- Timestamp:
- May 15, 2020, 2:27:39 PM (4 years ago)
- Branches:
- master, ctbto, dev
- Children:
- f20342a
- Parents:
- b936fd3
- Location:
- For_developers/Sphinx/source
- Files:
-
- 6 edited
-
Developers/gen_docu.rst (modified) (4 diffs)
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Support/faq.rst (modified) (1 diff)
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Support/known_bugs_issues.rst (modified) (3 diffs)
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changelog.rst (modified) (6 diffs)
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index.rst (modified) (4 diffs)
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support.rst (modified) (3 diffs)
Legend:
- Unmodified
- Added
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For_developers/Sphinx/source/Developers/gen_docu.rst
rb1674ed ra14839a 1 1 ******************** 2 Updat e Documentation2 Updating the documentation 3 3 ******************** 4 4 5 5 UNDER CONSTRUCTION 6 6 7 Additional Software7 Additional software 8 8 =================== 9 9 10 Developers working on ``flex_extract`` should make extensive use of the prepared test cases , unit tests andupdate the documentation. For this, some additional software is necessary:10 Developers working on ``flex_extract`` should make extensive use of the prepared test cases and unit tests, and should also update the documentation. For this, some additional software is necessary: 11 11 12 12 .. code-block:: sh … … 27 27 28 28 29 On line-documentation with Sphinx29 On-line documentation with Sphinx 30 30 ================================ 31 31 32 Use the scri ot ``gen_docu.sh`` to generate an update of the online documentation of the python component.32 Use the script ``gen_docu.sh`` to generate an update of the on-line documentation of the Python component. 33 33 34 It uses ``pyreverse`` to generate a class and a package diagram with graphvizand overwrites the old files in the developers directory.35 ``pyreverse`` creates ``dot`` files and with the ``dot`` program of the ``graphviz`` softwarethe ``png`` files are created. Everything happens in the Python source directory before moving them finally to the ``For_developers`` directory. The Sphinx source code has a ``_files`` directory which contains links to these ``png`` files and therefore they should not be renamed.34 It uses ``pyreverse`` to generate class and package diagrams with ``graphviz`` and overwrites the old files in the developers directory. 35 ``pyreverse`` creates ``dot`` files, and with the ``dot`` program of the ``graphviz`` software, the ``png`` files are created. Everything happens in the Python source directory before moving them finally to the ``For_developers`` directory. The Sphinx source code has a ``_files`` directory which contains links to these ``png`` files and therefore they should not be renamed. 36 36 37 37 … … 39 39 ------------------ 40 40 41 You might need to adapt the fonts path for the diagrams to a true 41 You might need to adapt the fonts path for the diagrams to a true-type font. Currently it is set to: 42 42 43 43 .. code-block:: bash … … 50 50 ------------------ 51 51 52 You might need to adapt the fonts path for the diagrams to a true 52 You might need to adapt the fonts path for the diagrams to a true-type font. Currently it is set to: 53 53 54 54 .. code-block:: bash -
For_developers/Sphinx/source/Support/faq.rst
rba99230 ra14839a 8 8 9 9 10 What can I do if I can't install the third 10 What can I do if I can't install the third-party libraries from distribution packages? 11 11 ====================================================================================== 12 12 13 This can be the case if the user does not have admin rights. 14 It is possible to install the necessary libraries locally from source. 15 For this case you should follow the following steps: 13 This can be the case if the user does not have admin rights and the sysadmins would not want to provide the libraries. 14 In this case, a workaround is to install the necessary libraries from source into a user directory, following these steps: 16 15 17 Installation hints:16 Steps to install libraries from source: 18 17 1. `Read Emoslib installation instructions <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_ 19 18 2. `Read ECMWF blog about gfortran <https://software.ecmwf.int/wiki/display/SUP/2015/05/11/Building+ECMWF+software+with+gfortran>`_ 20 19 3. `Install FFTW <http://www.fftw.org>`_ 21 4. `Install EMOSLIB <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_ ( 2 times make! one without any options and one with single precision option)20 4. `Install EMOSLIB <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_ (execute ``make`` two times! One time without any options, and another time with the single-precision option.) 22 21 5. `Install ECCODES <https://software.ecmwf.int/wiki/display/ECC>`_ 23 6. Register at Mars (:ref:`ref-registration`)22 6. Register for MARS access (:ref:`ref-registration`) 24 23 7. Install Web API's `CDS API <https://cds.climate.copernicus.eu/api-how-to>`_ and `ECMWF Web API <https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home>`_ 25 8. Check LD_LIBRARY_PATH environment variable if it contains all paths tothe libs26 9. Check available python packages (e.g. import eccodes / import grib_api / import ecmwfapi)24 8. Check whether LD_LIBRARY_PATH environment variable contains the paths to all the libs 25 9. Check available Python packages (e.g. ``import eccodes`` / ``import grib_api`` / ``import ecmwfapi``) 27 26 10. Start test retrieval (:ref:`ref-test-local`) 28 27 11. Install ``flex_extract`` (:doc:`../installation`) -
For_developers/Sphinx/source/Support/known_bugs_issues.rst
r3f383fe ra14839a 15 15 --------------------------------------------------------------------- 16 16 17 See ticket `#263 <https://www.flexpart.eu/ticket/263>`_ on flexpart.eu for information. 17 See ticket `#263 <https://www.flexpart.eu/ticket/263>`_ on flexpart.eu for information. Fixed in v7.1.1. 18 18 19 19 … … 21 21 -------------------------------------------------------------- 22 22 23 See ticket `#264 <https://www.flexpart.eu/ticket/264>`_ on flexpart.eu for information. 23 See ticket `#264 <https://www.flexpart.eu/ticket/264>`_ on flexpart.eu for information. Fixed in v7.1.1. 24 24 25 25 26 ECCODES Error Code 250 26 27 ---------------------- 27 28 28 If you get an error message from ECCODES with code 250, lo cking like this:29 If you get an error message from ECCODES with code 250, looking like this: 29 30 30 31 .. code-block:: bash … … 38 39 39 40 then you have set a wrong maximum level in the :literal:`CONTROL` file! 40 It is important to properly select the maximum level depending on the data set you would like to retrieve. The following model level definitions (number of model levels available) are limited to [16, 19, 31, 40, 50, 60, 62, 91, 137]. The ERA-Interim data set uses 62 model levels and *ERA5* as well as *CERA-20C* uses 137. The operational data set uses different model levels depending on the date. For example, on the 25/06/2013 the operational system started to use 137 model levels. Therefore, everytime you extract data from a date later than 25/06/2013 you have to select LEVEL=137 in the :literal:`CONTROL` file or define a LEVELLIST=1/to/137. Of course you can stop before the top of the atmosphere, such as 60/to/137, but you have to select the maximum level number as the last one. Table 2 in the `scientific model description paper <https://www.geosci-model-dev-discuss.net/gmd-2019-358/>`_ gives an overview of the level lists and the corresponding introducstion date. 41 It is important to properly select the maximum level depending on the data set you would like to retrieve. Only the following values of the number of model levels available are valid: 16, 19, 31, 40, 50, 60, 62, 91, 137. 42 43 The ERA-Interim data set uses 62 model levels and *ERA5* as well as *CERA-20C* uses 137. 44 45 The operational data sets use different numbers, depending on the date. For example, from 25/06/2013 on, 137 model levels were used in the operational system. Therefore, every time you extract data from a date later than 25/06/2013 you have to select LEVEL=137 in the :literal:`CONTROL` file, or you have to define LEVELLIST=1/to/137. Of course, you can stop before the top of the atmosphere, such as 60/to/137, but you have to include the maximum level number (i. e., the lowest level, see note below!) number as the last one. Table 2 in the `scientific model description paper <https://www.geosci-model-dev-discuss.net/gmd-2019-358/>`_ gives an overview of the level lists and the corresponding date they were introduced. 41 46 42 47 43 48 .. note:: 44 49 45 Remember that model level 1 corresponds to the top of the atmosphere and then increases in the direction of the surface.50 Be aware that the ECMWF model counts the levels from the top of the atmosphere downward to the surface. Level 1 is the topmost level, and e.g. 137 would be the level closest to the ground. -
For_developers/Sphinx/source/changelog.rst
rb1674ed ra14839a 20 20 * corrected naming of makefiles and Fortran program executable in online documentation 21 21 * adapted checking for ``GATEWAY`` and ``DESTINATION`` parameter 22 * fixed makefiles to use f90 Fortran files for ECMWF server22 * fixed Fortran makefiles to use the .f90 files on ECMWF servers 23 23 24 24 … … 42 42 * applied PEP8 style guide 43 43 * use of genshi templates 44 * modularization of python source code44 * modularization of Python source code 45 45 * upgrade from grib_api to ecCodes 46 * completely revised/refactored python section46 * completely revised/refactored Python section 47 47 * restructured program directories 48 48 * Fortran program name changed from ``CONVERT2`` to ``calc_etadot`` … … 60 60 ######### 61 61 62 * diverseproblems with ERA 5 retrieval63 * diverseproblems with CERA-20C retrieval62 * various problems with ERA 5 retrieval 63 * various problems with CERA-20C retrieval 64 64 * BASETIME retrieval option 65 65 * `CONVERT2` FORTRAN program: initialise fields to 0. … … 74 74 ############ 75 75 76 * output of marsrequests to an extra file (debugging and documentation)76 * output of MARS requests to an extra file (debugging and documentation) 77 77 * CERA-20C download 78 78 * ERA 5 download … … 87 87 ############ 88 88 89 * Python 89 * Python-based version 90 90 91 91 Changes 92 92 ####### 93 93 94 * korn shell scripts were substituted by python scripts94 * korn shell scripts substituted by Python scripts 95 95 96 96 .. _ref-v60: … … 99 99 ------------------- 100 100 101 * old version which should no longer be used anymore101 * old version which should no longer be used -
For_developers/Sphinx/source/index.rst
rb1674ed ra14839a 8 8 ================================================= 9 9 10 ``Flex_extract`` is an open-source software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to serve as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.10 ``Flex_extract`` is an open-source software to retrieve meteorological fields from the MARS archive of the European Centre for Medium-Range Weather Forecasts (ECMWF) to serve as input for the FLEXTRA/FLEXPART atmospheric transport modelling system. 11 11 12 12 .. raw:: html … … 32 32 <ul> 33 33 <li><a href="ecmwf_data.html">Overview</a></li> 34 <li><a href="Ecmwf/access.html">Access Modes</a></li>35 <li><a href="Ecmwf/ec-links.html">Link Collection</a></li>34 <li><a href="Ecmwf/access.html">Access modes</a></li> 35 <li><a href="Ecmwf/ec-links.html">Link collection</a></li> 36 36 </ul> 37 37 </td> … … 43 43 <ul> 44 44 <li><a href="Documentation/overview.html">Overview</a></li> 45 <li><a href="Documentation/input.html">Control & Input Data</a></li>46 <li><a href="Documentation/output.html">Output Data</a></li>45 <li><a href="Documentation/input.html">Control & input data</a></li> 46 <li><a href="Documentation/output.html">Output data</a></li> 47 47 </ul> 48 48 </td> … … 77 77 <h2><a href="dev_guide.html">Developer</a></h2> 78 78 <ul> 79 <li><a href="Developers/gen_docu.html">Update Documentation</a></li>80 81 <li><a href=""></a><Placeholder></li> 79 <li><a href="Developers/gen_docu.html">Updateing the documentation</a></li> 80 <!-- <li><a href=""></a><Placeholder></li> 81 <li><a href=""></a><Placeholder></li>--> 82 82 </ul> 83 83 </td> -
For_developers/Sphinx/source/support.rst
rba99230 ra14839a 16 16 .. _ticket system: https://www.flexpart.eu/report/1 17 17 18 The community website http ://flexpart.eucontains a19 `ticket system`_ which can be used to report any issue or a proposition for a new feature.18 The community website https://flexpart.eu/ contains a 19 `ticket system`_ which can be used to report any issue or to propose new features. 20 20 21 The tickets can be viewed by anyone, to create a ticket a registration is necessary. Since the automatic registration is unavailable, please send an email to the ``flexpart.eu[at]zamg.ac.at`` and you will receive your credentials ( with some delay).21 The tickets can be viewed by anyone, to create a ticket a registration is necessary. Since the automatic registration is unavailable, please send an email to the ``flexpart.eu[at]zamg.ac.at`` and you will receive your credentials (possibly with some delay). Event though a category "Support" is available, in most cases asking questions in the mailing list (see next paragraph below) will be more appropriate. 22 22 23 23 … … 27 27 ------------ 28 28 29 The mailing list is mainly for the ``FLEXPART`` users to ask questions or share experiences regarding the whole ``FLEXPART`` process with the community. This can be a lot faster than asking only the developers for help. Since ``flex_extract`` is a preprocessor to ``FLEXPART`` this is the right place to ask for help.29 A mailing list exists for the ``FLEXPART`` users to ask questions or share experiences with the community, regarding the whole ``FLEXPART`` process. This may be faster than asking only the developers for help through tickets. Since ``flex_extract`` is a preprocessor to ``FLEXPART`` this is the right place to ask for help. 30 30 31 Additionally, from time to time, there will be announcements for all FLEXPART users, such as new release versions of ``FLEXPART`` or ``flex_extract``. 32 33 Just write a mail to: ``flexpart[at]lists.univie.ac.at`` 31 New release versions of ``FLEXPART`` or ``flex_extract`` or other important annoucements will also be made through this mailling list. 32 The subscription process is explained at the bottom of https://www.flexpart.eu/wiki/RegisteredUser. Once subscribed, write e-mail to ``flexpart[at]lists.univie.ac.at`` to post to the list. 34 33 35 34 … … 41 40 To properly report a problem or bug, please provide as much information as possible. 42 41 This includes: 43 44 * the flex_extract version 45 * a flex_extract log file (output of submit.py script) 46 * the CONTROL file 47 * the commandline arguments or run(_local).sh settings and 48 * a description of the environment you used (Unix/Linux version, library version, application mode, etc.). 42 * the ``flex_extract`` version 43 * a ``flex_extract log`` file (output of ``submit.py`` script) 44 * the ``CONTROL`` file 45 * the command-line arguments or ``run(_local).sh`` settings and 46 * a description of your environment (Unix/Linux version, library version, application mode, etc.). 49 47 50 48
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