Changeset 5bee29a in flex_extract.git for Documentation/html/_sources
- Timestamp:
- Jun 1, 2020, 8:41:16 PM (4 years ago)
- Branches:
- master, ctbto, dev
- Children:
- 8a53342
- Parents:
- a9d33f6
- Location:
- Documentation/html/_sources
- Files:
-
- 15 edited
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Developers/gen_docu.rst.txt (modified) (4 diffs)
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Documentation/Input/fortran_makefile.rst.txt (modified) (2 diffs)
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Documentation/Input/jobscript.rst.txt (modified) (1 diff)
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Documentation/Input/setup.rst.txt (modified) (1 diff)
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Documentation/disagg.rst.txt (modified) (3 diffs)
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Installation/local.rst.txt (modified) (7 diffs)
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Installation/remote.rst.txt (modified) (1 diff)
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Support/faq.rst.txt (modified) (1 diff)
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Support/known_bugs_issues.rst.txt (modified) (3 diffs)
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changelog.rst.txt (modified) (6 diffs)
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documentation.rst.txt (modified) (2 diffs)
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index.rst.txt (modified) (5 diffs)
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installation.rst.txt (modified) (4 diffs)
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quick_start.rst.txt (modified) (1 diff)
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support.rst.txt (modified) (3 diffs)
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Documentation/html/_sources/Developers/gen_docu.rst.txt
rb1674ed r5bee29a 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 -
Documentation/html/_sources/Documentation/Input/fortran_makefile.rst.txt
r5920b7f r5bee29a 16 16 | Files to be used as they are! 17 17 18 | **makefile_ecgate**: For use on ECMWF'sserver **ecgate**.19 | **makefile_cray**: For use on ECMWF's server**cca/ccb**.18 | **makefile_ecgate**: For use on the ECMWF server **ecgate**. 19 | **makefile_cray**: For use on the ECMWF servers **cca/ccb**. 20 20 21 21 | **Local mode** … … 24 24 | **makefile_fast**: For use with the gfortran compiler and optimisation mode. 25 25 | **makefile_debug**: For use with the gfortran compiler and debugging mode. Primarily for developers. 26 | **makefile_local_gfortran**: Linked to makefile_fast. Default value. 27 28 They can be found at ``flex_extract_vX.X/Source/Fortran/``, where ``vX.X`` should be substituted by the current flex_extract version number. 29 30 .. caution:: 31 It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these 32 ``makefiles`` if other than standard paths are used. 33 34 Thus, go to the ``Fortran`` source directory and open the ``makefile`` of your 35 choice, and check / modify with an editor of your choice: 36 37 .. code-block:: bash 38 39 cd flex_extract_vX.X/Source/Fortran 40 nedit makefile_fast 41 42 Set the paths to the ``eccodes`` library on your local machine, if necessary. 43 44 .. caution:: 45 This can vary from system to system. 46 It is suggested to use a command like 47 48 .. code-block:: bash 49 50 # for the ECCODES_INCLUDE_DIR path do: 51 $ dpkg -L libeccodes-dev | grep eccodes.mod 52 # for the ECCODES_LIB path do: 53 $ dpkg -L libeccodes-dev | grep libeccodes.so 54 55 to find out the path to the ``eccodes`` library. 56 57 Assign these paths to the parameters **ECCODES_INCLUDE_DIR** 58 and **ECCODES_LIB** in the makefile, and save it. 59 60 .. code-block:: bash 61 62 # these are the paths on Debian Buster: 63 ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/ 64 ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm 65 26 66 27 67 If you want to use another compiler than gfortran locally, you can still take ``makefile_fast``, 28 68 and adapt everything that is compiler-specific in this file. 29 30 For instructions on how to adapt the ``makefile`` (local application mode only),31 please see :ref:`ref-install-local`.32 69 33 70 -
Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
r5920b7f r5bee29a 139 139 mailfail ${USER} 140 140 mailops ${USER} 141 makefile Makefile.gfortran142 141 marsclass EP 143 142 maxstep 0 -
Documentation/html/_sources/Documentation/Input/setup.rst.txt
r5920b7f r5bee29a 174 174 Valid targets: local | ecgate | cca , the latter two 175 175 are at ECMWF (default: None) 176 --makefile MAKEFILE Name of Makefile to use for compiling the Fortran 177 program (default: None) 176 --makefile MAKEFILE Name of makefile to compile the Fortran 177 code. (default depends on `target`: local - makefile_local_gfortran, 178 ecgate - makefile_ecgate, cca - makefile_cray) 178 179 --ecuid ECUID The user id at ECMWF. (default: None) 179 180 --ecgid ECGID The group id at ECMWF. (default: None) -
Documentation/html/_sources/Documentation/disagg.rst.txt
r5920b7f r5bee29a 17 17 :widths: 5,15,5,10 18 18 19 LSP, "large-scale precipitation", " :math:`m`", "modified linear interpolation"20 CP, "convective precipitation", " :math:`m`", "modified linear interpolation"21 SSHF, "surface sensible heat flux", " :math:`J m^{-2}`", "bicubic interpolation"22 EWSS, "eastward turbulent surface stress", " :math:`N m^{-2} s`", "bicubic interpolation"23 NSSS, "northward turbulent surface stress", " :math:`N m^{-2} s`", "bicubic interpolation"24 SSR, "surface net solar radiation", " :math:`J m^{-2}`", "bicubic interpolation"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" 25 25 26 26 … … 62 62 63 63 64 Disaggregation is done for four adjacent time spans (:math:`a_0, a_1, a_2, a_3`) which generates a new, disaggregated value which is output at the central point of the four adjacent timespans.64 Disaggregation is done for four adjacent time intervals (:math:`a_0, a_1, a_2, a_3`) which generates a new, disaggregated value which is output at the central point of the four adjacent time intervals. 65 65 66 66 .. math:: 67 67 68 p_{ac} &= 0.5 *a_1\\68 p_{ac} &= 0.5 a_1\\ 69 69 m &= a_0 + a_2 > 0.\\ 70 p_{ac}(m) &= a_1(m) *a_2(m) / (a_0(m) + a_2(m))\\70 p_{ac}(m) &= a_1(m) a_2(m) / (a_0(m) + a_2(m))\\ 71 71 p_{bd} &= 0.5 * a_2\\ 72 72 m &= a_1 + a_3 > 0.\\ 73 p_{bd}(m) &= a_1(m) *a_2(m) / (a_1(m) + a_3(m))\\73 p_{bd}(m) &= a_1(m) a_2(m) / (a_1(m) + a_3(m))\\ 74 74 75 75 76 This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards. If one of the four original time spans has a value below 0, it is set to 0 prior to the calculation.76 This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards. If one of the four original time intervals has a value below 0, it is set to 0 prior to the calculation. 77 77 78 78 .. math:: … … 162 162 The accumulated values for the other variables are first divided by the number of hours and 163 163 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 spans (: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 timespans.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. 165 165 166 166 .. math:: -
Documentation/html/_sources/Installation/local.rst.txt
r5920b7f r5bee29a 11 11 12 12 13 .. _Python 3: https://docs.python.org/3/ 14 .. _Python3: https://www.python.org/downloads/ 15 .. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section 16 13 .. _Python3: https://www.python.org/ 14 .. _Anaconda Python3: https://www.anaconda.com/distribution/ 17 15 .. _numpy: http://www.numpy.org/ 18 16 .. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home 19 17 .. _cdsapi: https://cds.climate.copernicus.eu/api-how-to 20 18 .. _genshi: https://genshi.edgewall.org/ 21 .. _eccodes for python: https://p ackages.debian.org/sid/python3-eccodes19 .. _eccodes for python: https://pypi.org/project/eccodes-python/ 22 20 .. _eccodes for conda: https://anaconda.org/conda-forge/eccodes 23 21 .. _gfortran: https://gcc.gnu.org/wiki/GFortran … … 30 28 .. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans 31 29 .. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf 32 .. _ECMWF 's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home30 .. _ECMWF instructions on gateway servers: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home 33 31 .. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives 34 32 .. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS 35 36 33 .. _download section: https://www.flexpart.eu/downloads 37 34 38 39 40 41 35 42 36 .. _ref-local-mode: 43 44 45 37 46 38 .. _ref-req-local: … … 54 46 and libraries, since the preparation of the extraction and the post-processing is done on the local machine: 55 47 56 +------------------------------------------------ -+-----------------+57 | Python part | Fortran part|58 +------------------------------------------------ -+-----------------+59 | 1. `Python3`_ | 1.`gfortran`_ |60 | 2. `numpy`_ | 2.`fftw3`_ |61 | 3. `genshi`_ | 3.`eccodes`_ |62 | 4. `eccodes for python`_ | 4.`emoslib`_ |63 | 5. `ecmwf-api-client`_ (everything except ERA5) ||64 | 6. `cdsapi`_ (just for ERA5 and member user) ||65 +------------------------------------------------ -+-----------------+48 +------------------------------------------------+----------------+ 49 | Python code | Fortran code | 50 +------------------------------------------------+----------------+ 51 | * `Python3`_ | * `gfortran`_ | 52 | * `numpy`_ | * `fftw3`_ | 53 | * `genshi`_ | * `eccodes`_ | 54 | * `eccodes for python`_ | * `emoslib`_ | 55 | * `ecmwf-api-client`_ (everything except ERA5) | | 56 | * `cdsapi`_ (just for ERA5 and member user) | | 57 +------------------------------------------------+----------------+ 66 58 67 59 … … 265 257 266 258 267 268 259 .. _ref-install-local: 269 260 … … 271 262 ================== 272 263 273 First, adapt the Fortran ``makefile`` for your environment (if necessary) and insert it into ``setup.sh`` script (see :ref:`Fortran Makefile <ref-convert>` for more information). 274 They can be found at ``flex_extract_vX.X/Source/Fortran/``, where ``vX.X`` should be substituted by the current flex_extract version number. 275 276 .. caution:: 277 It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these 278 ``makefiles`` if other than standard paths are used. 279 280 Thus, go to the ``Fortran`` source directory and open the ``makefile`` of your 281 choice, and check / modify with an editor of your choice: 282 283 .. code-block:: bash 284 285 cd flex_extract_vX.X/Source/Fortran 286 nedit makefile_fast 264 265 The Fortran program called ``calc_etadot`` will be compiled during the 266 installation process. A suitable makefile (``makefile_local_gfortran``) for the compilation is set by default. 267 This may be overwritten by the ``MAKEFILE`` parameter in ``setup.sh``. 268 269 However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup.sh`` 270 For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`. 271 287 272 288 Set the paths to the ``eccodes`` library on your local machine, if necessary.289 290 .. caution::291 This can vary from system to system.292 It is suggested to use a command like293 294 .. code-block:: bash295 296 # for the ECCODES_INCLUDE_DIR path do:297 $ dpkg -L libeccodes-dev | grep eccodes.mod298 # for the ECCODES_LIB path do:299 $ dpkg -L libeccodes-dev | grep libeccodes.so300 301 to find out the path to the ``eccodes`` library.302 303 Assign these paths to the parameters **ECCODES_INCLUDE_DIR**304 and **ECCODES_LIB** in the makefile, and save it.305 306 .. code-block:: bash307 308 # these are the paths on Debian Buster:309 ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/310 ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm311 312 313 The Fortran program called ``calc_etadot`` will be compiled during the314 installation process. Therefore, the name of the ``makefile`` to be used needs to be given in ``setup.sh``.315 316 273 In the root directory of ``flex_extract``, open the ``setup.sh`` script 317 274 with an editor and adapt the installation parameters in the section labelled with … … 330 287 # 331 288 TARGET='local' 332 MAKEFILE='makefile_fast'333 289 ECUID=None 334 290 ECGID=None … … 357 313 Install flex_extract_v7.1 software at local in directory <path-to-flex_extract>/flex_extract_v7.1 358 314 359 Using makefile: makefile_ fast315 Using makefile: makefile_local_gfortran 360 316 gfortran -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./rwgrib2.f90 361 317 gfortran -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./phgrreal.f90 -
Documentation/html/_sources/Installation/remote.rst.txt
rb1674ed r5bee29a 48 48 49 49 +---------------------------+-----------------+ 50 | Python part | Fortran part|50 | Python code | Fortran code | 51 51 +---------------------------+-----------------+ 52 52 | * `Python3`_ | * `gfortran`_ | -
Documentation/html/_sources/Support/faq.rst.txt
rba99230 r5bee29a 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`) -
Documentation/html/_sources/Support/known_bugs_issues.rst.txt
r3f383fe r5bee29a 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. -
Documentation/html/_sources/changelog.rst.txt
rb1674ed r5bee29a 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 -
Documentation/html/_sources/documentation.rst.txt
r5920b7f r5bee29a 1 ************* 2 Documentation3 ************* 1 ************************ 2 Code-Level Documentation 3 ************************ 4 4 5 5 Overview (under construction) 6 6 7 Control & input data7 Scripts, control & input data 8 8 9 9 Output data (under construction) … … 11 11 Disaggregation of flux data (under construction) 12 12 13 Vertical coordinate(under construction)13 Vertical wind (under construction) 14 14 - methods (GAUSS, ETA, OMEGA) 15 15 - calc_etadot -
Documentation/html/_sources/index.rst.txt
r5920b7f r5bee29a 4 4 contain the root `toctree` directive. 5 5 6 ================================================= 7 Welcome to ``flex_extract``'s user documentation!8 ================================================= 6 =================================================== 7 Welcome to the ``flex_extract`` Documentation! 8 =================================================== 9 9 10 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. … … 14 14 <table style="width:100%;"> 15 15 <tr> 16 <td style="width:30%;height:150px;">17 <div style="width:100%;height:60px;margin-left:20%;position:relative;">18 <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/install_icon.png">19 </div>20 <h2><a href="installation.html">Installation</a></h2>21 <ul>22 <li><a href="installation.html#ref-requirements">Environment requirements</a></li>23 <li><a href="installation.html#ref-download">Download flex_extract</a></li>24 <li><a href="installation.html#ref-install-fe">Install flex_extract</a></li>25 </ul>26 </td>27 16 <td style="width:30%;height:150px;"> 28 17 <div style="width:100%;height:60px;margin-left:20%;position:relative;"> … … 38 27 <td style="width:30%;height:150px;"> 39 28 <div style="width:100%;height:60px;margin-left:20%;position:relative;"> 40 <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/ prog_icon.png">29 <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/install_icon.png"> 41 30 </div> 42 <h2><a href=" documentation.html">Documentation</a></h2>31 <h2><a href="installation.html">Installation</a></h2> 43 32 <ul> 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>33 <li><a href="installation.html#ref-requirements">Dependencies</a></li> 34 <li><a href="installation.html#ref-download">Download flex_extract</a></li> 35 <li><a href="installation.html#ref-install-fe">Install flex_extract</a></li> 47 36 </ul> 48 </td> 49 </tr> 50 <tr> 37 </td> 51 38 <td style="width:30%;height:150px;"> 52 39 <div style="width:100%;height:60px;margin-left:20%;position:relative;"> 53 40 <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/guide_icon.png"> 54 41 </div> 55 <h2><a href="quick_start.html"> Quick Start</a></h2>42 <h2><a href="quick_start.html">Usage</a></h2> 56 43 <ul> 57 44 <li><a href="quick_start.html#job-preparation">Job preparation</a></li> 58 <li><a href="quick_start.html#selection-and-adjustment-of-control-files"> HandlingCONTROL files</a></li>45 <li><a href="quick_start.html#selection-and-adjustment-of-control-files">CONTROL files</a></li> 59 46 <li><a href="quick_start.html#hints-for-definition-of-some-parameter-combinations">Hints on parameter combinations</a></li> 60 47 </ul> 61 </td> 48 </td> </tr> 49 <tr> 50 <td style="width:30%;height:150px;"> 51 <div style="width:100%;height:60px;margin-left:20%;position:relative;"> 52 <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/prog_icon.png"> 53 </div> 54 <h2><a href="documentation.html">Code-level documentation</a></h2> 55 <ul> 56 <li><a href="Documentation/overview.html">Overview</a></li> 57 <li><a href="Documentation/input.html">Scripts, control & input data</a></li> 58 <li><a href="Documentation/output.html">Output data</a></li> 59 </ul> 60 </td> 62 61 <td style="width:30%;height:150px;"> 63 62 <div style="width:100%;height:60px;margin-left:20%;position:relative;"> … … 75 74 <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/dev_icon.png"> 76 75 </div> 77 <h2><a href="dev_guide.html">Developer </a></h2>76 <h2><a href="dev_guide.html">Developer guide</a></h2> 78 77 <ul> 79 <li><a href="Developers/gen_docu.html">Updat eing the documentation</a></li>78 <li><a href="Developers/gen_docu.html">Updating the documentation</a></li> 80 79 <li><a href=""></a><Placeholder></li> 81 80 <li><a href=""></a><Placeholder></li> … … 132 131 :caption: Table of Contents: 133 132 133 ecmwf_data 134 134 installation 135 135 quick_start 136 ecmwf_data137 136 documentation 138 137 evaluation -
Documentation/html/_sources/installation.rst.txt
r5920b7f r5bee29a 135 135 ============ 136 136 137 The software required for running``flex_extract`` depends on the :doc:`Documentation/Overview/app_modes` and therefore is described in the respective specific installation sections.137 The software required to run ``flex_extract`` depends on the :doc:`Documentation/Overview/app_modes` and therefore is described in the respective specific installation sections. 138 138 139 139 Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries. 140 We tested ``flex_extract`` with the python3 package from the the GNU/Linux distribution and Anaconda Python. The required python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).141 142 Before installing the system packages check the availability with ``dpkg -s <package-name> | grep Status`` or ``rpm -q <package_name>``, depending on your system. For example:140 We tested ``flex_extract`` with the Python3 package from the the GNU/Linux distribution and Anaconda Python. The required Python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.). 141 142 Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system)``rpm -q <package_name>``. For example: 143 143 144 144 .. code-block:: sh … … 150 150 151 151 152 153 154 155 152 .. _ref-install-fe: 156 153 … … 183 180 Installation/local 184 181 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 182 203 183 … … 206 186 207 187 Some users might wish to incorporate ``flex_extract`` directly into the ``FLEXPART`` distribution. Then the installation path has to be changed by setting the parameter `installdir` in the ``setup.sh`` file to the ``script`` directory in the ``FLEXPART`` root directoy. 208 209 210 211 212 213 214 215 188 216 189 -
Documentation/html/_sources/quick_start.rst.txt
r5920b7f r5bee29a 1 ***** ******2 Quick Start 3 ***** ******1 ***** 2 Usage 3 ***** 4 4 5 5 ``flex_extract`` is a command-line tool. In the first versions, it was started via a korn shell script and since version 6, the entry point was a python script. From version 7.1, a bash shell script was implemented to call ``flex_extract`` with the command-line parameters. -
Documentation/html/_sources/support.rst.txt
rba99230 r5bee29a 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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