Changeset 11723


Ignore:
Timestamp:
2019-10-18T14:33:36+02:00 (11 months ago)
Author:
nicolasmartin
Message:

Review of INSTALL.rst

Files:
4 deleted
7 edited
1 moved

Legend:

Unmodified
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  • NEMO/trunk/CHANGES.rst

    r11713 r11723  
    1 ************* 
    2 Release Notes 
    3 ************* 
     1******* 
     2Changes 
     3******* 
    44 
    55.. todo:: 
    66 
    7    Complete "Release Notes" 
     7   List the main additions of the the new release 
  • NEMO/trunk/INSTALL.rst

    r11708 r11723  
    1010 
    1111| The NEMO source code is written in *Fortran 95* and 
    12   some of its prerequisite tools and libraries are already included in the ``./ext`` subdirectory. 
     12  some of its prerequisite tools and libraries are already included in the download. 
    1313| It contains the AGRIF_ preprocessing program ``conv``; the FCM_ build system and 
    1414  the IOIPSL_ library for parts of the output. 
     
    4040   This will limit MPI features to those defined within the MPI-2 standard 
    4141   (but will lose some performance benefits). 
    42  
    43 Specifics for NetCDF and HDF 
    44 ---------------------------- 
    45  
    46 NetCDF and HDF versions from . 
    47 However access to all the options available with the XIOS IO-server will require 
    48 the parallel IO support of these libraries which can be unavailable. 
    49  
    50 | **To satisfy these requirements, it is common to have to compile from source 
    51   in this order HDF (C library) then NetCDF (C and Fortran libraries)** 
    52 | It is also necessary to compile these libraries with the same version of the MPI implementation that 
    53   both NEMO and XIOS (see below) are compiled and linked with. 
    54  
    55 .. hint:: 
    56  
    57    | It is difficult to define the options for the compilation as 
    58      they differ from one architecture to another according to 
    59      the hardware used and the software installed. 
    60    | The following is provided without any warranty 
    61  
    62    .. code-block:: console 
    63  
    64       $ ./configure [--{enable-fortran,disable-shared,enable-parallel}] ... 
    65  
    66    It is recommended to build the tests ``--enable-parallel-tests`` and run them with ``make check`` 
    67  
    68 Particular versions of these libraries may have their own restrictions. 
    69 State the following requirements for netCDF-4 support: 
    70  
    71 .. caution:: 
    72  
    73    | When building NetCDF-C library versions older than 4.4.1, use only HDF5 1.8.x versions. 
    74    | Combining older NetCDF-C versions with newer HDF5 1.10 versions will create superblock 3 files 
    75      that are not readable by lots of older software. 
    76  
    77 Extract and install XIOS 
    78 ======================== 
    79  
    80 With the sole exception of running NEMO in mono-processor mode 
    81 (in which case output options are limited to those supported by the ``IOIPSL`` library), 
    82 diagnostic outputs from NEMO are handled by the third party ``XIOS`` library. 
    83 This can be used in two different modes: 
    84  
    85 - *attached* - Every NEMO process also acts as a XIOS server 
    86 - *detached* - Every NEMO process runs as a XIOS client. 
    87   Output is collected and collated by external, stand-alone XIOS server processors. 
    88  
    89 .. important:: 
    90  
    91    In either case, XIOS needs to be compiled before NEMO, 
    92    since the libraries are needed to successfully create the NEMO executable. 
    93  
    94 Instructions on how to obtain and install the software can be found on the :xios:`XIOS wiki<wiki>`. 
    95  
    96 .. hint:: 
    97  
    98    It is recommended to use XIOS version 2.5. 
    99    This version should be more stable (in terms of future code changes) than the XIOS trunk. 
    100    It is also the version used by the NEMO system team when testing all developments and new releases. 
    101  
    102    This particular version has its own branch and can be checked out and downloaded with: 
    103  
    104    .. code:: console 
    105  
    106       $ svn co https://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 
    107  
    108 Download the NEMO source code 
    109 ============================= 
    110  
    111 .. code:: console 
    112  
    113    $ svn co https://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk 
    114  
    115 Description of directory tree 
    116 ----------------------------- 
    117  
    118 +-----------+------------------------------------------------------------+ 
    119 | Folder    | Purpose                                                    | 
    120 +===========+============================================================+ 
    121 | ``arch``  | Settings (per architecture-compiler pair)                  | 
    122 +-----------+------------------------------------------------------------+ 
    123 | ``cfgs``  | :doc:`Reference configurations <configurations>`           | 
    124 +-----------+------------------------------------------------------------+ 
    125 | ``doc``   | - ``latex``    : LaTex source code for ref. manuals        | 
    126 |           | - ``namelists``: k start guide                             | 
    127 |           | - ``rst``      : ReST files for quick start guide          | 
    128 +-----------+------------------------------------------------------------+ 
    129 | ``ext``   | Dependencies included (``AGRIF``, ``FCM`` & ``IOIPSL``)    | 
    130 +-----------+------------------------------------------------------------+ 
    131 | ``mk``    | Building  routines                                         | 
    132 +-----------+------------------------------------------------------------+ 
    133 | ``src``   | Modelling routines                                         | 
    134 |           |                                                            | 
    135 |           | - ``ICE``: |NEMO-ICE| for sea ice                          | 
    136 |           | - ``NST``: AGRIF for embedded zooms                        | 
    137 |           | - ``OCE``: |NEMO-OCE| for ocean dynamics                   | 
    138 |           | - ``TOP``: |NEMO-MBG| for tracers                          | 
    139 +-----------+------------------------------------------------------------+ 
    140 | ``tests`` | :doc:`Test cases <test_cases>` (unsupported)               | 
    141 +-----------+------------------------------------------------------------+ 
    142 | ``tools`` | :doc:`Utilities <tools>` to [pre|post]process data         | 
    143 +-----------+------------------------------------------------------------+ 
    144  
    145 Setup your architecture configuration file 
    146 ========================================== 
    147  
    148 All compiler options in NEMO are controlled using files in 
    149 ``./arch/arch-'my_arch'.fcm`` where 'my_arch' is the name of the computing 
    150 architecture.  It is recommended to copy and rename an configuration file from 
    151 an architecture similar to your owns. You will need to set appropriate values 
    152 for all of the variables in the file. In particular the FCM variables: 
    153 ``%NCDF_HOME``; ``%HDF5_HOME`` and ``%XIOS_HOME`` should be set to the 
    154 installation directories used for XIOS installation. 
    155  
    156 .. code-block:: sh 
    157  
    158         %NCDF_HOME           /opt/local 
    159         %HDF5_HOME           /opt/local 
    160         %XIOS_HOME           /Users/$( whoami )/xios-2.5 
    161         %OASIS_HOME          /not/defined 
    162  
    163 Compile and create NEMO executable 
    164 ================================== 
    165  
    166 The main script to compile and create executable is called makenemo and located in the CONFIG directory, it is used to identify the routines you need from the source code, to build the makefile and run it. 
    167 As an example, compile GYRE with 'my_arch' to create a 'MY_GYRE' configuration: 
    168  
    169 .. code-block:: sh 
    170  
    171    ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' 
    172  
    173 The image below shows the structure and some content of "MY_CONFIG" directory from the launching of the configuration creation (directories and fundamental files created by makenemo). 
    174  
    175 +------------+----------------------------------------------------+ 
    176 | Folder     | Purpose                                            | 
    177 +============+====================================================+ 
    178 | ``BLD``    |                                                    | 
    179 +------------+----------------------------------------------------+ 
    180 | ``EXP00``  |                                                    | 
    181 +------------+----------------------------------------------------+ 
    182 | ``EXPREF`` |                                                    | 
    183 +------------+----------------------------------------------------+ 
    184 | ``MY_SRC`` |                                                    | 
    185 +------------+----------------------------------------------------+ 
    186 | ``WORK``   |                                                    | 
    187 +------------+----------------------------------------------------+ 
    188  
    189 Folder with the symbolic links to all unpreprocessed routines considered in the configuration 
    190 Compilation folder (executables, headers files, libraries, preprocessed routines, flags, …) 
    191 Computation folder for running the model (namelists, xml, executables and inputs-outputs) 
    192 Folder intended to contain your customised routines (modified from initial ones or new entire routines) 
    193  
    194 After successful execution of makenemo command, the executable called opa is created in the EXP00 directory (in the example above, the executable is created in CONFIG/MY_GYRE/EXP00). 
    195  
    196 More makenemo options 
    197 --------------------- 
    198  
    199 ``makenemo`` has several other options that can control which source files are selected and 
    200 the operation of the build process itself. 
    201 These are:: 
    202  
    203    Optional: 
    204       -d  Set of new sub-components (space separated list from ./src directory) 
    205       -e  Path for alternative patch  location (default: 'MY_SRC' in configuration folder) 
    206       -h  Print this help 
    207       -j  Number of processes to compile (0: no build) 
    208       -n  Name for new configuration 
    209       -s  Path for alternative source location (default: 'src' root directory) 
    210       -t  Path for alternative build  location (default: 'BLD' in configuration folder) 
    211       -v  Level of verbosity ([0-3]) 
    212  
    213 These options can be useful for maintaining several code versions with only minor differences but 
    214 they should be used sparingly. 
    215 Note however the ``-j`` option which should be used more routinely to speed up the build process. 
    216 For example: 
    217  
    218 .. code-block:: sh 
    219  
    220         ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' -j 8 
    221  
    222 which will compile up to 8 modules simultaneously. 
    223  
    224  
    225 Default behaviour 
    226 ----------------- 
    227  
    228 At the first use, you need the -m option to specify the architecture 
    229 configuration file (compiler and its options, routines and libraries to 
    230 include), then for next compilation, it is assumed you will be using the 
    231 same compiler.  If the –n option is not specified the last compiled configuration 
    232 will be used. 
    233  
    234 Tools used during the process 
    235 ----------------------------- 
    236  
    237 *   functions.sh : bash functions used by makenemo, for instance to create the WORK directory 
    238 *   cfg.txt : text list of configurations and source directories 
    239 *   bld.cfg : FCM rules to compile 
    240  
    241 Examples 
    242 -------- 
    243  
    244 .. code-block:: sh 
    245  
    246         echo "Example to install a new configuration MY_CONFIG"; 
    247         echo "with OPA_SRC and LIM_SRC_2 "; 
    248         echo "makenemo -n MY_CONFIG -d \"OPA_SRC LIM_SRC_2\""; 
    249         echo ""; 
    250         echo "Available configurations :"; cat ${CONFIG_DIR}/cfg.txt; 
    251         echo ""; 
    252         echo "Available unsupported (external) configurations :"; cat ${CONFIG_DIR}/uspcfg.txt; 
    253         echo ""; 
    254         echo "Example to remove bad configuration "; 
    255         echo "./makenemo -n MY_CONFIG clean_config"; 
    256         echo ""; 
    257         echo "Example to clean "; 
    258         echo "./makenemo clean"; 
    259         echo ""; 
    260         echo "Example to list the available keys of a CONFIG "; 
    261         echo "./makenemo list_key"; 
    262         echo ""; 
    263         echo "Example to add and remove keys"; 
    264         echo "./makenemo add_key \"key_iomput key_mpp_mpi\" del_key \"key_agrif\" "; 
    265         echo ""; 
    266         echo "Example to add and remove keys for a new configuration, and do not compile"; 
    267         echo "./makenemo -n MY_CONFIG -j0 add_key \"key_iomput key_mpp_mpi\" del_key \"key_agrif\" "; 
    268  
    269 Running the model 
    270 ================= 
    271  
    272 Once makenemo has run successfully, the opa executable is available in ``CONFIG/MY_CONFIG/EXP00`` 
    273 For the reference configurations, the EXP00 folder also contains the initial input files (namelists, \*xml files for the IOs…). If the configuration also needs NetCDF input files, this should be downloaded here from the corresponding tar file, see Users/Reference Configurations 
    274  
    275 .. code-block:: sh 
    276  
    277         cd 'MY_CONFIG'/EXP00 
    278         mpirun -n $NPROCS ./opa    # $NPROCS is the number of processes ; mpirun is your MPI wrapper 
    279  
    280  
    281 Viewing and changing list of active CPP keys 
    282 ============================================ 
    283  
    284 For a given configuration (here called MY_CONFIG), the list of active CPP keys can be found in: 
    285  
    286 .. code-block:: sh 
    287  
    288         ./cfgs/'MYCONFIG'/cpp_'MY_CONFIG'.fcm 
    289  
    290  
    291 This text file can be edited to change the list of active CPP keys. Once changed, one needs to recompile opa executable using makenemo command in order for this change to be taken in account. 
    292 Note that most NEMO configurations will need to specify the following CPP keys: 
    293 ``key_iomput`` and ``key_mpp_mpi`` 
    294  
    295 .. Links and substitutions 
    29642 
    29743.. |OpenMPI| replace:: *OpenMPI* 
     
    30046.. _MPICH:   https://www.mpich.org 
    30147.. |NetCDF|  replace:: *Network Common Data Form (NetCDF)* 
    302 .. _NetCDF:  https://www.unidata.ucar.edu/downloads/netcdf 
     48.. _NetCDF:  https://www.unidata.ucar.edu 
    30349.. |HDF|     replace:: *Hierarchical Data Form (HDF)* 
    304 .. _HDF:     https://www.hdfgroup.org/downloads 
     50.. _HDF:     https://www.hdfgroup.org 
     51 
     52Specifics for NetCDF and HDF 
     53---------------------------- 
     54 
     55NetCDF and HDF versions from official repositories may have not been compiled with MPI support. 
     56However access to all the options available with the XIOS IO-server will require 
     57the parallelism of these libraries. 
     58 
     59| **To satisfy these requirements, it is common to have to compile from source 
     60  in this order HDF (C library) then NetCDF (C and Fortran libraries)** 
     61| It is also necessary to compile these libraries with the same version of the MPI implementation that 
     62  both NEMO and XIOS (see below) have been compiled and linked with. 
     63 
     64.. hint:: 
     65 
     66   | It is difficult to define the options for the compilation as 
     67     they differ from one architecture to another according to 
     68     the hardware used and the software installed. 
     69   | The following is provided without any warranty 
     70 
     71   .. code-block:: console 
     72 
     73      $ ./configure [--{enable-fortran,disable-shared,enable-parallel}] ... 
     74 
     75   It is recommended to build the tests ``--enable-parallel-tests`` and run them with ``make check`` 
     76 
     77Particular versions of these libraries may have their own restrictions. 
     78State the following requirements for netCDF-4 support: 
     79 
     80.. caution:: 
     81 
     82   | When building NetCDF-C library versions older than 4.4.1, use only HDF5 1.8.x versions. 
     83   | Combining older NetCDF-C versions with newer HDF5 1.10 versions will create superblock 3 files 
     84     that are not readable by lots of older software. 
     85 
     86Extract and install XIOS 
     87======================== 
     88 
     89With the sole exception of running NEMO in mono-processor mode 
     90(in which case output options are limited to those supported by the ``IOIPSL`` library), 
     91diagnostic outputs from NEMO are handled by the third party ``XIOS`` library. 
     92It can be used in two different modes: 
     93 
     94:*attached*:  Every NEMO process also acts as a XIOS server 
     95:*detached*:  Every NEMO process runs as a XIOS client. 
     96  Output is collected and collated by external, stand-alone XIOS server processors. 
     97 
     98Instructions on how to install XIOS can be found on its :xios:`wiki<>`. 
     99 
     100.. hint:: 
     101 
     102   It is recommended to use XIOS 2.5 release. 
     103   This version should be more stable (in terms of future code changes) than the XIOS trunk. 
     104   It is also the one used by the NEMO system team when testing all developments and new releases. 
     105 
     106   This particular version has its own branch and can be checked out with: 
     107 
     108   .. code:: console 
     109 
     110      $ svn co https://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 
     111 
     112Download and install the NEMO code 
     113================================== 
     114 
     115Checkout the NEMO sources 
     116------------------------- 
     117 
     118.. code:: console 
     119 
     120   $ svn co https://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk 
     121 
     122Description of 1\ :sup:`st` level tree structure 
     123------------------------------------------------ 
     124 
     125+-----------+----------------------------------------+ 
     126| ``arch``  | Compilation settings                   | 
     127+-----------+----------------------------------------+ 
     128| ``cfgs``  | :doc:`Reference configurations <cfgs>` | 
     129+-----------+----------------------------------------+ 
     130| ``doc``   | :doc:`Documentation <doc>`             | 
     131+-----------+----------------------------------------+ 
     132| ``ext``   | Dependencies included                  | 
     133|           | (``AGRIF``, ``FCM`` & ``IOIPSL``)      | 
     134+-----------+----------------------------------------+ 
     135| ``mk``    | Compilation scripts                    | 
     136+-----------+----------------------------------------+ 
     137| ``src``   | :doc:`Modelling routines <src>`        | 
     138+-----------+----------------------------------------+ 
     139| ``tests`` | :doc:`Test cases <tests>`              | 
     140|           | (unsupported)                          | 
     141+-----------+----------------------------------------+ 
     142| ``tools`` | :doc:`Utilities <tools>`               | 
     143|           | to {pre,post}process data              | 
     144+-----------+----------------------------------------+ 
     145 
     146Setup your architecture configuration file 
     147------------------------------------------ 
     148 
     149All compiler options in NEMO are controlled using files in :file:`./arch/arch-'my_arch'.fcm` where 
     150``my_arch`` is the name of the computing architecture 
     151(generally following the pattern ``HPCC-compiler`` or ``OS-compiler``). 
     152It is recommended to copy and rename an configuration file from an architecture similar to your owns. 
     153You will need to set appropriate values for all of the variables in the file. 
     154In particular the FCM variables: 
     155``%NCDF_HOME``; ``%HDF5_HOME`` and ``%XIOS_HOME`` should be set to 
     156the installation directories used for XIOS installation 
     157 
     158.. code-block:: sh 
     159 
     160   %NCDF_HOME    /usr/local/path/to/netcdf 
     161   %HDF5_HOME    /usr/local/path/to/hdf5 
     162   %XIOS_HOME    /home/$( whoami )/path/to/xios-2.5 
     163   %OASIS_HOME   /home/$( whoami )/path/to/oasis 
     164 
     165Create and compile a new configuration 
     166====================================== 
     167 
     168The main script to {re}compile and create executable is called ``makenemo`` located at 
     169the root of the working copy. 
     170It is used to identify the routines you need from the source code, to build the makefile and run it. 
     171As an example, compile a :file:`MY_GYRE` configuration from GYRE with 'my_arch': 
     172 
     173.. code-block:: sh 
     174 
     175   ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' 
     176 
     177Then at the end of the configuration compilation, 
     178:file:`MY_GYRE` directory will have the following structure. 
     179 
     180+------------+----------------------------------------------------------------------------+ 
     181| Directory  | Purpose                                                                    | 
     182+============+============================================================================+ 
     183| ``BLD``    | BuiLD folder: target executable, headers, libs, preprocessed routines, ... | 
     184+------------+----------------------------------------------------------------------------+ 
     185| ``EXP00``  | Run   folder: link to executable, namelists, ``*.xml`` and IOs             | 
     186+------------+----------------------------------------------------------------------------+ 
     187| ``EXPREF`` | Files under version control only for :doc:`official configurations <cfgs>` | 
     188+------------+----------------------------------------------------------------------------+ 
     189| ``MY_SRC`` | New routines or modified copies of NEMO sources                            | 
     190+------------+----------------------------------------------------------------------------+ 
     191| ``WORK``   | Links to all raw routines from :file:`./src` considered                    | 
     192+------------+----------------------------------------------------------------------------+ 
     193 
     194After successful execution of ``makenemo`` command, 
     195the executable called `nemo` is available in the :file:`EXP00` directory 
     196 
     197More ``makenemo`` options 
     198------------------------- 
     199 
     200``makenemo`` has several other options that can control which source files are selected and 
     201the operation of the build process itself. 
     202 
     203.. literalinclude:: ../../../makenemo 
     204   :language: text 
     205   :lines: 119-143 
     206   :caption: Output of ``makenemo -h`` 
     207 
     208These options can be useful for maintaining several code versions with only minor differences but 
     209they should be used sparingly. 
     210Note however the ``-j`` option which should be used more routinely to speed up the build process. 
     211For example: 
     212 
     213.. code-block:: sh 
     214 
     215        ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' -j 8 
     216 
     217will compile up to 8 processes simultaneously. 
     218 
     219Default behaviour 
     220----------------- 
     221 
     222At the first use, 
     223you need the ``-m`` option to specify the architecture configuration file 
     224(compiler and its options, routines and libraries to include), 
     225then for next compilation, it is assumed you will be using the same compiler. 
     226If the ``-n`` option is not specified the last compiled configuration will be used. 
     227 
     228Tools used during the process 
     229----------------------------- 
     230 
     231* ``functions.sh`` : bash functions used by ``makenemo``, for instance to create the WORK directory 
     232* ``cfg.txt`` : text list of configurations and source directories 
     233* ``bld.cfg`` : FCM rules to compile 
     234 
     235Examples 
     236-------- 
     237 
     238.. literalinclude:: ../../../makenemo 
     239   :language: text 
     240   :lines: 146-153 
     241 
     242Running the model 
     243================= 
     244 
     245Once ``makenemo`` has run successfully, 
     246the ``nemo`` executable is available in ``./cfgs/MY_CONFIG/EXP00``. 
     247For the reference configurations, the ``EXP00`` folder also contains the initial input files 
     248(namelists, ``*.xml`` files for the IOs, ...). 
     249If the configuration needs other input files, they have to be placed here. 
     250 
     251.. code-block:: sh 
     252 
     253   cd 'MY_CONFIG'/EXP00 
     254   mpirun -n $NPROCS ./nemo   # $NPROCS is the number of processes 
     255                              # mpirun is your MPI wrapper 
     256 
     257Viewing and changing list of active CPP keys 
     258============================================ 
     259 
     260For a given configuration (here called ``MY_CONFIG``), 
     261the list of active CPP keys can be found in :file:`./cfgs/'MYCONFIG'/cpp_MY_CONFIG.fcm` 
     262 
     263This text file can be edited by hand or with ``makenemo`` to change the list of active CPP keys. 
     264Once changed, one needs to recompile ``nemo`` in order for this change to be taken in account. 
     265Note that most NEMO configurations will need to specify the following CPP keys: 
     266``key_iomput`` for IOs and ``key_mpp_mpi`` for parallelism. 
  • NEMO/trunk/README.rst

    r11713 r11723  
    2020These physical core engines are described in 
    2121their respective `reference publications <#project-documentation>`_ that 
    22 must be cited for any work related to their use (see :doc:`citations`). 
     22must be cited for any work related to their use (see :doc:`cite`). 
    2323 
    2424Assets and solutions 
     
    3030- Create :doc:`embedded zooms<zooms>` seamlessly thanks to 2-way nesting package AGRIF_. 
    3131- Opportunity to integrate an :doc:`external biogeochemistry model<tracers>` 
    32 - Versatile :doc:`data assimilation<data_assimilation>` 
    33 - Generation of :doc:`diagnostics<diagnostics>` through effective XIOS_ system 
    34 - Roll-out Earth system modeling with :doc:`coupling interface<coupling>` based on OASIS_ 
     32- Versatile :doc:`data assimilation<da>` 
     33- Generation of :doc:`diagnostics<diags>` through effective XIOS_ system 
     34- Roll-out Earth system modeling with :doc:`coupling interface<cplg>` based on OASIS_ 
    3535 
    36 Several :doc:`built-in configurations<configurations>` are provided to 
     36Several :doc:`built-in configurations<cfgs>` are provided to 
    3737evaluate the skills and performances of the model which 
    3838can be used as templates for setting up a new configurations (:file:`./cfgs`). 
    3939 
    40 The user can also checkout available :doc:`idealized test cases<test_cases>` that 
     40The user can also checkout available :doc:`idealized test cases<tests>` that 
    4141address specific physical processes (:file:`./tests`). 
    4242 
  • NEMO/trunk/cfgs/AGRIF_DEMO/README.rst

    r10460 r11723  
    2020=========== 
    2121 
    22 Activating AGRIF requires to append the cpp key ``key_agrif`` at compilation time:  
     22Activating AGRIF requires to append the cpp key ``key_agrif`` at compilation time: 
    2323 
    2424.. code-block:: sh 
     
    5454depends on the number of ghost cells as illustrated by the (attempted) drawing below for nbghostcells=1 and 
    5555nbghostcells=3. 
    56 The grid refinement is 3 and nxfin is the number of child grid points in i-direction.   
     56The grid refinement is 3 and nxfin is the number of child grid points in i-direction. 
    5757 
    5858.. image:: _static/agrif_grid_position.jpg 
     
    6262boundary data exchange and update being only performed between root and child grids. 
    6363Use of east-west periodic or north-fold boundary conditions is not allowed in child grids either. 
    64 Defining for instance a circumpolar zoom in a global model is therefore not possible.  
     64Defining for instance a circumpolar zoom in a global model is therefore not possible. 
    6565 
    6666Preprocessing 
     
    9292      rn_sponge_dyn = 2880.   !  coefficient for dynamics sponge layer [m2/s] 
    9393      ln_chk_bathy  = .false. !  =T  check the parent bathymetry 
    94    /              
     94   / 
    9595 
    9696where sponge layer coefficients have to be chosen according to the child grid mesh size. 
    9797The sponge area is hard coded in NEMO and applies on the following grid points: 
    98 2 x refinement factor (from i=1+nbghostcells+1 to i=1+nbghostcells+sponge_area)  
     982 x refinement factor (from i=1+nbghostcells+1 to i=1+nbghostcells+sponge_area) 
    9999 
    100 References 
    101 ========== 
     100.. rubric:: References 
    102101 
    103102.. bibliography:: zooms.bib 
    104    :all: 
    105    :style: unsrt 
    106    :labelprefix: A 
    107    :keyprefix: a- 
     103   :all: 
     104   :style: unsrt 
     105   :labelprefix: A 
     106   :keyprefix: a- 
  • NEMO/trunk/cfgs/README.rst

    r11708 r11723  
    296296while lateral boundary conditions for dynamical fields have 3 days time frequency. 
    297297 
    298 References 
    299 ========== 
    300  
    301 .. bibliography:: configurations.bib 
     298.. rubric:: References 
     299 
     300.. bibliography:: cfgs.bib 
    302301   :all: 
    303302   :style: unsrt 
    304303   :labelprefix: C 
    305  
    306 .. Links and substitutions 
  • NEMO/trunk/src/TOP/README.rst

    r11713 r11723  
    208208 
    209209The overall data structure (Fortran type) is based on the general one defined for NEMO core in the SBC component 
    210 (see details in ``SBC`` Chapter of :doc:`Reference Manual <citations>` on Input Data specification). 
     210(see details in ``SBC`` Chapter of :doc:`Reference Manual <cite>` on Input Data specification). 
    211211 
    212212Input fields are prescribed within ``&namtrc_dta`` (with ``sn_trcdta`` structure), 
     
    230230Note that, the Lateral Open Boundaries conditions are applied on 
    231231the segments defined for the physical core of NEMO 
    232 (see ``BDY`` description in the :doc:`Reference Manual <citations>`). 
     232(see ``BDY`` description in the :doc:`Reference Manual <cite>`). 
    233233 
    234234:file:`namelist_trc` 
     
    286286:file:`trcwri_my_trc.F90` 
    287287   This routine performs the output of the model tracers (only those defined in ``&namtrc``) using 
    288    IOM module (see chapter “Output and Diagnostics” in the :doc:`Reference Manual <citations>`). 
     288   IOM module (see chapter “Output and Diagnostics” in the :doc:`Reference Manual <cite>`). 
    289289   It is possible to place here the output of additional variables produced by the model, 
    290290   if not done elsewhere in the code, using the call to ``iom_put``. 
  • NEMO/trunk/tests/README.rst

    r10605 r11723  
    1313 
    1414.. contents:: 
    15    :local: 
     15   :local: 
    1616 
    1717Procedure 
     
    3434------------------------------ 
    3535 
    36 There no requirement of specific input file for the test_cases presented here. The XIOS xml input files and namelist are already setup correctly.  
     36There no requirement of specific input file for the test_cases presented here. The XIOS xml input files and namelist are already setup correctly. 
    3737For detailed description and Jupyter notebook, the reader is directed on 
    3838the `NEMO test cases repository <http://github.com/NEMO-ocean/NEMO-examples>`_ 
     
    4242ICE_AGRIF 
    4343========= 
    44    
     44 
    4545  This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel 
    4646  over a slab ocean (i.e. one ocean layer), and with an AGRIF zoom (1:3) in the center 
    47   The purpose of this configuration is to test the advection of the ice patch in   
     47  The purpose of this configuration is to test the advection of the ice patch in 
    4848  and across the AGRIF boundary 
    4949  One can either impose ice velocities or ice-atm. stresses and let rheology define velocities 
     
    5454VORTEX 
    5555====== 
    56    
     56 
    5757  This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom. 
    5858  It is implemented here with an online refined subdomain (1:3) out of which the vortex propagates. 
    5959  It serves as a benchmark for quantitative estimates of nesting errors as in Debreu et al. (2012) :cite:`DEBREU2012`, 
    6060  Penven et al. (2006) :cite:`PENVEN2006` or Spall and Holland (1991) :cite:`SPALL1991`. 
    61    
     61 
    6262  The animation below (sea level anomaly in meters) illustrates with two 1:2 successively nested grids how 
    6363  the vortex smoothly propagates out of the refined grids. 
    64    
     64 
    6565  .. image:: _static/VORTEX_anim.gif 
    6666 
     
    6969 
    7070  The purpose of this test case is to evaluate the impact of various schemes and new development with the iceshelf cavities circulation and melt. 
    71   This configuration served as initial assesment of the ice shelf module in Losh et al. (2008) :cite:`LOSCH2008` and Mathiot et al. (2017) :cite:`MATHIOT2017`.  
     71  This configuration served as initial assesment of the ice shelf module in Losh et al. (2008) :cite:`LOSCH2008` and Mathiot et al. (2017) :cite:`MATHIOT2017`. 
    7272  The default setup is the one described `here <http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf>`_. 
    73    
     73 
    7474  The figure below (meridional overturning circulation) illustrates the circulation generated after 10000 days by the ice shelf melting (ice pump). 
    7575 
     
    8282  by Haidvogel and Beckmann (1999) :cite:`HAIDVOGEL1999` for testing advection schemes in ocean circulation models. 
    8383  It has been used by several authors including Burchard and Bolding (2002) :cite:`BURCHARD2002` and Ilicak et al. (2012) :cite:`ILICAK2012`. 
    84   The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes  
     84  The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes 
    8585  and/or subgrid closures on spurious interior mixing. 
    8686 
     
    9292======== 
    9393 
    94   The OVERFLOW experiment illustrates the impact of different choices of numerical schemes  
    95   and/or subgrid closures on spurious interior mixing close to bottom topography.  
    96   The OVERFLOW experiment is adapted from the non-rotating overflow configuration described  
     94  The OVERFLOW experiment illustrates the impact of different choices of numerical schemes 
     95  and/or subgrid closures on spurious interior mixing close to bottom topography. 
     96  The OVERFLOW experiment is adapted from the non-rotating overflow configuration described 
    9797  in Haidvogel and Beckmann (1999) :cite:`HAIDVOGEL1999` and further used by Ilicak et al. (2012) :cite:`ILICAK2012`. 
    9898  Here we can assess the behaviour of the second-order tracer advection scheme FCT2 and fortht-order FCT4, z-coordinate and sigma coordinate (...). 
     
    105105=== 
    106106 
    107   A set of simple closed basin geometries for testing the Wetting and drying capabilities.  
     107  A set of simple closed basin geometries for testing the Wetting and drying capabilities. 
    108108  Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge. 
    109    
     109 
    110110  Below the animation of the test case 7. This test case is a simple linear slope with a mid-depth shelf with an open boundary forced with a sinusoidally varying ssh. 
    111111  This test case has been introduced to emulate a typical coastal application with a tidally forced open boundary with an adverse SSH gradient that, when released, creates a surge up the slope. 
     
    123123ICE_ADV2D 
    124124========= 
    125    
     125 
    126126  This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel 
    127127  over a slab ocean (i.e. one ocean layer). 
     
    130130  (for now, Prather and Ultimate-Macho from 1st to 5th order), 
    131131  especially the occurence of overshoots in ice thickness 
    132    
     132 
    133133 
    134134ICE_ADV1D 
    135135========= 
    136    
     136 
    137137  This experiment is the classical Schar & Smolarkiewicz (1996) test case :cite:`SCHAR1996`, 
    138138  which has been used in :cite:`LIPSCOMB2004`, 
     
    141141  The purpose of this configuration is to test the caracteristics of advection schemes available in the sea-ice code 
    142142  (for now, Prather and Ultimate-Macho from 1st to 5th order), 
    143   especially the constitency between concentration, thickness and volume, and the preservation of initial shapes.   
     143  especially the constitency between concentration, thickness and volume, and the preservation of initial shapes. 
    144144 
    145 References 
    146 ========== 
     145.. rubric:: References 
    147146 
    148 .. bibliography:: test_cases.bib 
    149    :all: 
    150    :style: unsrt 
    151    :labelprefix: T 
     147.. bibliography:: tests.bib 
     148   :all: 
     149   :style: unsrt 
     150   :labelprefix: T 
  • utils/build/makenemo

    r11692 r11723  
    5252# - TOOLS_DIR   :   "    "    " 
    5353# - NEMO_DIR    :   "    "    " 
    54 # - REMOTE_CTL  : URL link to a remote resource list for an external configuration  
     54# - REMOTE_CTL  : URL link to a remote resource list for an external configuration 
    5555#                 which is not part of the reference suite 
    56 # - LOCAL_REF   : Nearest reference configuration to an external configuration  
     56# - LOCAL_REF   : Nearest reference configuration to an external configuration 
    5757#                 which is not part of the reference suite 
    5858#                 (used to populate work directories if remote access is not available) 
     
    119119Usage: 
    120120------ 
    121 ./makenemo -[aru] CONFIG -m ARCH [-[dehjntv] ...] [{list_key,clean,clean_config}] [{add_key,del_key} ...] 
    122  
    123 Mandatory: 
    124    -m   Computing architecture (./arch), FCM file describing the compilation settings 
     121./makenemo -[aru] CONFIG -m ARCH [-[dehjntv] ...] [{list_key,clean,clean_config}] 
     122                                                  [{add_key,del_key} ...] 
     123 
     124Mandatory 
     125   -m    Computing architecture (./arch), FCM file describing the compilation settings 
     126 
    125127   and one of the following option (use 'all' arg to list available items) 
    126    -r   Reference configuration (./cfgs), proven with long-term support until the EOL of the release 
    127    -a   Academic test case (./tests), ready to use at the release start without guarantee or support over time 
    128    -u   Scripted remote configuration (see ./tests/rmt_cfgs.txt) 
    129  
    130 Optional: 
    131    -d   New set of sub-components (list from ./src directory) 
    132    -e   Path for alter patch  location (default: 'MY_SRC' in configuration folder) 
    133    -h   Print this help 
    134    -j   Number of processes to compile (0: dry run with no build) 
    135    -n   Name for new configuration 
    136    -s   Path for alter source location (default: 'src' root directory) 
    137    -t   Path for alter build  location (default: 'BLD' in configuration folder) 
    138    -v   Level of verbosity ([0-3]) 
    139  
    140 Examples: 
     128 
     129   -r    Reference configuration (./cfgs), proven with long-term support 
     130   -a    Academic test case (./tests), ready-to-use configuration with no support over time 
     131   -u    Scripted remote configuration (see ./tests/rmt_cfgs.txt) 
     132 
     133Optional 
     134   -d    New set of sub-components (subfolders from ./src directory) 
     135   -e    Path for alter patch  location (default: 'MY_SRC' in configuration folder) 
     136   -h    Print this help 
     137   -j    Number of processes to compile (0: dry run with no build) 
     138   -n    Name for new configuration 
     139   -s    Path for alter source location (default: 'src' root directory) 
     140   -t    Path for alter build  location (default: 'BLD' in configuration folder) 
     141   -v    Level of verbosity ([0-3]) 
     142 
     143Examples 
    141144   ¤ Configuration creation 
    142         Build          : ./makenemo -[aru] ... [...] 
     145        Build          : ./makenemo         -[aru] ... [...] 
    143146        Copy           : ./makenemo -n ...  -[aru] ... [...] 
    144147   ¤ Configuration management 
    145         List CPP keys  : ./makenemo [...] list_key 
    146         Add-Remove keys: ./makenemo [...] add_key '...' del_key '...' 
    147         Fresh start    : ./makenemo [...] clean 
    148         Erasure        : ./makenemo [...] clean_config 
     148        List CPP keys  : ./makenemo -n ... list_key 
     149        Add-Remove keys: ./makenemo -n ... add_key '...' del_key '...' 
     150        Fresh start    : ./makenemo -n ... clean 
     151        Removal        : ./makenemo -n ... clean_config 
    149152EOF 
    150153            exit 0       ;; 
     
    258261else 
    259262 
    260    ## Reuse a working cfg   
     263   ## Reuse a working cfg 
    261264   if [[ -f ${CONFIG_DIR}/work_cfgs.txt && $( grep "${TML_CONF} " ${CONFIG_DIR}/work_cfgs.txt ) ]]; then 
    262265      conf_file=work_cfgs.txt 
     
    362365 
    363366   ## if AGRIF we do a first preprocessing 
    364    if [[ ${#x_c} -eq 0 && "$AGRIFUSE" -eq 1 ]]; then  
     367   if [[ ${#x_c} -eq 0 && "$AGRIFUSE" -eq 1 ]]; then 
    365368      fcm build --ignore-lock -j 1 ${COMPIL_DIR}/bld_preproagr.cfg ||{ cd - ; exit 1 ;} 
    366369      echo '' 
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