Changeset 10596


Ignore:
Timestamp:
2019-01-28T17:20:19+01:00 (18 months ago)
Author:
nicolasmartin
Message:

Fixes for a unsuccessful Python Sphinx building, no more warnings but still crashing

Location:
NEMO/trunk
Files:
6 edited

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/INSTALL.rst

    r10559 r10596  
    1313  include: the AGRIF preprocessing program "conv"; the FCM build system and the  
    1414  IOIPSL library for parts of the output. 
    15 | 
    1615- Other requirements that your system needs to provide include: a Perl 5 interpreter; a modern 
    1716  Fortran compiler (ifort, gfortran, pgfortran, ...) and (in most cases) a MPI library 
     
    2423  features to those defined within the MPI-2 standard (but will lose some performance 
    2524  benefits). 
    26 | 
     25 
    2726The following prerequisites may already be installed or be available from the 
    2827official repositories of your Linux distribution. However access to all the 
     
    4039netcdf-c-4.6.2 and netcdf-fortran-4.4.4, state the following requirements for netCDF-4 support: 
    4140 
    42 * HDF5 1.8.9 or later. 
    43 * HDF5 1.10.1 or later. 
    44 * zlib 1.2.5 or later (for netCDF-4 compression) 
    45 * curl 7.18.0 or later (for DAP remote access client support) 
    46  
    47 | 
     41- HDF5 1.8.9 or later. 
     42- HDF5 1.10.1 or later. 
     43- zlib 1.2.5 or later (for netCDF-4 compression) 
     44- curl 7.18.0 or later (for DAP remote access client support) 
     45 
    4846`Important Note: When building netCDF-C library versions older than 4.4.1, 
    4947use only HDF5 1.8.x versions. Combining older netCDF-C versions with newer 
  • NEMO/trunk/README.rst

    r10592 r10596  
    6060 
    6161..  _external biogeochemistry model : http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/TOP/TOP-UserQuickGuide 
    62 .. _NEMO : https://www.nemo-ocean.eu/ 
    63 .. _OASIS : https://portal.enes.org/oasis 
    64 .. _XIOS : http://forge.ipsl.jussieu.fr/ioserver 
    65 .. _AGRIF : https://www-ljk.imag.fr/MOISE/AGRIF/ 
    6662.. _working groups : https://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups 
    6763.. _reference documentation : https://www.nemo-ocean.eu/bibliography/documentation/ 
     
    6965.. _associated projects : https://www.nemo-ocean.eu/projects/ 
    7066.. _bibliography : https://www.nemo-ocean.eu/wp-content/plugins/wp-bibtexbrowser/bibtexbrowser.php?bib=nemo.bib 
    71 .. _CMCC : https://www.cmcc.it/ 
    72 .. _CNRS : http://www.cnrs.fr/ 
    73 .. _MOI : https://www.mercator-ocean.fr 
    74 .. _Met Office : https://www.metoffice.gov.uk/ 
    75 .. _NERC : https://nerc.ukri.org/ 
    76 .. _`NEMO manual` : http://zenodo.org/badge/DOI/10.5281/zenodo.1464816.svg 
    77 .. _`NEMO guide` : http://zenodo.org/badge/DOI/10.5281/zenodo.1475325.svg 
    78 .. _`SI3 manual` : http://zenodo.org/badge/DOI/10.5281/zenodo.1471689.svg 
    79 .. _`TOP manual` : http://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg 
    80  
  • NEMO/trunk/RELEASE_NOTES.rst

    r10595 r10596  
    1212  - Lateral melting 
    1313  - Melt ponds: constant or :doi:`10.1175/JCLI-D-11-00078.1 <Holland et al. 2012>` formulation (and soon topographic melt ponds) 
    14   - Ice-atm. drags from :doi:`10.1029/2012JD017630 <Lupkes et al. 2012>` (depending on ice concentration) or 
    15     :doi:`10.1002/2014JD022418 <Lupkes et al. 2015>` (depending on sea ice concentration and atm. stability) 
     14  - Ice-atm. drags from :doi:`10.1029/2012JD017630 <Lupkes et al. 2012>` (depending on ice concentration) or :doi:`10.1002/2014JD022418 <Lupkes et al. 2015>` (depending on sea ice concentration and atm. stability) 
    1615  - Landfast ice (:doi:`10.1002/2016JC012006 <Lemieux et al. 2016>`) 
    1716 
     
    6463The first test cases available for now are: 
    6564- ``CANAL``: east-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex) 
    66 - ``ICE_AGRIF``: east-west + north-south periodic channel. 
    67   The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys. 
    68 - ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. 
    69   The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. 
    70   The exact original setup is described ​here. 
    71 - ``LOCK-EXCHANGE``:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. 
    72   It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). 
    73   The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing 
    74 - ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. 
    75   It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012) 
    76 - ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. 
    77   It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. 
    78   It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991) 
    79 - ``WAD``: a set of simple closed basin geometries for testing the Wetting and drying capabilities. 
    80   Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge.  
     65- ``ICE_AGRIF``: east-west + north-south periodic channel. The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys. 
     66- ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. The exact original setup is described ​here. 
     67- ``LOCK-EXCHANGE``:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing 
     68- ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012) 
     69- ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991) 
     70- ``WAD``: a set of simple closed basin geometries for testing the Wetting and drying capabilities. Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge.  
    8171 
    8272New Reference configurations 
     
    9787- The passive tracers transport component was redesigned toward a modular structure and users can enable each module directly through logical flags in namelist_top (no more fortran macros!). 
    9888- :doc:`tracers <TOP on-line user documentation>` 
    99 - TOP currently accounts for the following 5 modules: 
    100   CFC contains inorganic carbon tracers (CFC11/CFC12/SF6), 
    101   MY_TRC is a template for new modules (or external couplings), 
    102   AGE deals with water age tracking, 
    103   C14 as a radiocarbon passive tracer, and 
    104   the companion ecosystem model PISCES. 
     89- ``TOP`` currently accounts for the following 5 modules: 
     90  ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6), 
     91  ``MY_TRC`` is a template for new modules (or external couplings), 
     92  ``AGE`` deals with water age tracking, 
     93  ``C14`` as a radiocarbon passive tracer, and 
     94  the companion ecosystem model ``PISCES``. 
    10595- A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer. 
    10696- A new configuration, named ORCA2_OFF_TRC, was created to provide a benchmark simulation environment to deal with inert carbon tracers dynamics by exploiting the offline coupling with NEMO. 
  • NEMO/trunk/cfgs/README.rst

    r10541 r10596  
    8080-------- 
    8181 
    82 GYRE_BFM shares the same physical setup of GYRE_PISCES_, but NEMO is coupled with the `BFM <http://www.bfm-community.eu/>`_ biogeochemical model as described in :trac:`source:/NEMO/trunk/cfgs/GYRE_BFM/README`. 
     82GYRE_BFM shares the same physical setup of GYRE_PISCES_, but NEMO is coupled with the `BFM <http://www.bfm-community.eu/>`_ biogeochemical model as described in :forge:`browser/NEMO/trunk/cfgs/GYRE_BFM/README`. 
    8383 
    8484 
     
    100100  / 
    101101 
    102 Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and vertical levels are set by ``jpkglo``. The specific code changes can be inspected at :trac:`source:/NEMO/trunk/src/OCE/USR`  
     102Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and vertical levels are set by ``jpkglo``. The specific code changes can be inspected at :forge:`browser/NEMO/trunk/src/OCE/USR`  
    103103 
    104104**Running GYRE as a benchmark** :  this simple configuration can be used as a benchmark since it is easy to increase resolution, with the drawback of getting results that have a very limited physical meaning. 
     
    217217Note that, this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that model mesh is not varying in time and it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that requires the provision of bbl coefficients through ``sn_ubl`` and ``sn_vbl`` fields. 
    218218 
    219 It is also possible to activate PISCES model (see ORCA2_OFF_PISCES_) or a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.`` (and adaptation of :trac:`source:/NEMO/trunk/src/TOP/MY_TRC` routines). 
     219It is also possible to activate PISCES model (see ORCA2_OFF_PISCES_) or a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.`` (and adaptation of :forge:`browser/NEMO/trunk/src/TOP/MY_TRC` routines). 
    220220 
    221221In addition, the offline module (OFF) allows for the provision of further fields: 
     
    235235 
    236236 
    237 More details can be found by inspecting the offline data manager at :trac:`source:/NEMO/trunk/src/OFF/dtadyn.F90` 
     237More details can be found by inspecting the offline data manager at :forge:`browser/NEMO/trunk/src/OFF/dtadyn.F90` 
    238238 
    239239 
  • NEMO/trunk/doc/rst/source/NEMO_guide.rst

    r10593 r10596  
    4343   zooms 
    4444   coupling 
    45    assimilation 
     45   data_assimilation 
    4646   tracers 
    4747 
  • NEMO/trunk/doc/rst/source/global.rst

    r10557 r10596  
    1616.. Institutes 
    1717 
    18 .. _CMCC:           http://www.cmcc.it  
    19 .. _CNRS:           http://www.cnrs.fr 
    20 .. _Mercator Ocean: http://www.mercator-ocean.fr 
    21 .. _Met Office:     http://www.metoffice.gov.uk 
    22 .. _MOI:            http://www.mercator-ocean.fr 
    23 .. _NERC:           http://nerc.ukri.org 
     18.. _CMCC:           https://www.cmcc.it  
     19.. _CNRS:           https://www.cnrs.fr 
     20.. _Mercator Ocean: https://www.mercator-ocean.fr 
     21.. _Met Office:     https://www.metoffice.gov.uk 
     22.. _MOI:            https://www.mercator-ocean.fr 
     23.. _NERC:           https://nerc.ukri.org 
    2424 
    2525.. Models / Softwares 
    2626 
    27 .. _AGRIF: http://agrif.imag.fr 
    28 .. _OASIS: http://verc.enes.org/oasis 
    29 .. _XIOS:  http://forge.ipsl.jussieu.fr/ioserver 
     27.. _AGRIF: https://agrif.imag.fr 
     28.. _OASIS: https://portal.enes.org/oasis 
     29.. _XIOS:  https://forge.ipsl.jussieu.fr/ioserver 
    3030 
    3131.. NEMO 
    3232 
    33 .. _NEMO:          http://www.nemo-ocean.eu 
    34 .. _NEMO strategy: http://doi.org/10.5281/zenodo.1471663 
    35 .. _NEMO guide:    http://doi.org/10.5281/zenodo.1475325 
    36 .. _NEMO manual:   http://doi.org/10.5281/zenodo.1464816 
    37 .. _SI3 manual:    http://doi.org/10.5281/zenodo.1471689 
    38 .. _TOP manual:    http://doi.org/10.5281/zenodo.1471700 
     33.. _NEMO:          https://www.nemo-ocean.eu 
     34.. _NEMO strategy: https://doi.org/10.5281/zenodo.1471663 
     35.. _NEMO guide:    https://doi.org/10.5281/zenodo.1475325 
     36.. _NEMO manual:   https://doi.org/10.5281/zenodo.1464816 
     37.. _SI3 manual:    https://doi.org/10.5281/zenodo.1471689 
     38.. _TOP manual:    https://doi.org/10.5281/zenodo.1471700 
Note: See TracChangeset for help on using the changeset viewer.