Changeset 10187


Ignore:
Timestamp:
2018-10-09T19:08:59+02:00 (20 months ago)
Author:
nicolasmartin
Message:

Push draft versions of RST root files

Location:
NEMO/trunk
Files:
1 added
3 edited

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/INSTALL.rst

    r9596 r10187  
    1 Install the modelling framework (NEMO and XIOS) 
     1===================== 
     2Install the framework 
     3===================== 
    24 
    3 Last edition: 2018-02-14 21:32 CET by nicolasmartin 
     5.. contents:: \ 
     6   :local: 
     7       
     8Dependencies 
     9============ 
    410 
    5     Extract the NEMO code 
    6         Description of NEMOGCM directory tree 
    7     Extract and install XIOS 
    8     Setup your architecture configuration file 
    9     Compile and create NEMO executable 
    10         More options 
    11         Default behaviour 
    12         Tools used during the process 
    13         Examples 
    14     Running the model 
    15     Viewing and changing list of active CPP keys 
     11| The NEMO source code is written in Fortran 95 and part of its dependencies are already included (``./ext``): 
     12  AGRIF preprocessing program "conv", FCM build system and IOIPSL library for outputs. 
     13| And some Perl 5, Fortran compiler (ifort, gfortran, pgfortran, ...), MPI library (Open MPI or MPICH) 
    1614 
    17 Extract the NEMO code 
     15But The following dependencies should be from the official repositories of your Linux distribution but 
     16you will probably have to compile them from source for enabling parallel I/O support. 
    1817 
    19 Using your account registered here ('my_login' with password) 
     18- `HDF5`_   (C library) 
     19- `NetCDF`_ (C and Fortran libraries) 
     20 
     21Extract the source code 
     22======================= 
     23 
     24Download the source code  
    2025 
    2126.. code:: console 
    22 svn --username 'mylogin' co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2015/nemo_v3_6_STABLE/NEMOGCM 
    2327 
    24 Description of NEMOGCM directory tree 
     28   $ svn co http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/releases/release-4.0 
    2529 
    26 The image below shows the directory tree: 
     30Description of directory tree 
     31============================= 
    2732 
    28 simple table: 
    29     ARCH    Compilation option files, with format arch_compiler.fcm, the compiler name has to be provided with –m option 
    30     CONFIG  All configurations and a cpp.fcm file containing the list of CPP keys to each configuration 
    31     EXTERNAL    Package to implement an embedded model (AGRIF) 
    32     NEMO    FORTRAN source codes in several sub-directories 
    33     SETTE    Package to make tests to ensure the reproducibility and restartability of the code after changes 
    34     TOOLS    Useful softwares to different utilities 
     33+-----------+---------------------------------------------------------------+ 
     34| Folder    | Purpose                                                       | 
     35+===========+===============================================================+ 
     36| ``arch``  | Settings (per architecture-compiler pair)                     | 
     37+-----------+---------------------------------------------------------------+ 
     38| ``cfgs``  | Reference configurations                                      | 
     39+-----------+---------------------------------------------------------------+ 
     40| ``doc``   | - ``latex``: reference manuals for NEMO, SI\ :sup:`3`\  & TOP | 
     41|           | - ``rst``:   quick start guide                                | 
     42+-----------+---------------------------------------------------------------+ 
     43| ``ext``   | Dependencies included (AGRIF, FCM & IOIPSL)                   | 
     44+-----------+---------------------------------------------------------------+ 
     45| ``mk``    | Building  routines                                            | 
     46+-----------+---------------------------------------------------------------+ 
     47| ``src``   | Modelling routines                                            | 
     48|           |                                                               | 
     49|           | - ``ICE``: SI\ :sup:`3`\ for sea ice                          | 
     50|           | - ``NST``: AGRIF         for embedded zooms                   | 
     51|           | - ``OCE``: OPA           for ocean dynamics                   | 
     52|           | - ``MBG``: TOP           for tracers                          | 
     53+-----------+---------------------------------------------------------------+ 
     54| ``tests`` | Test cases                                                    | 
     55+-----------+---------------------------------------------------------------+ 
     56| ``tools`` | Utilities to [pre|post]process data                           | 
     57+-----------+---------------------------------------------------------------+ 
    3558 
    3659Extract and install XIOS 
     60======================== 
    3761 
    3862Diagnostic outputs from NEMO are handled by the third party XIOS library. 
     
    4266 
    4367When you compile NEMO you will need to specify the following CPP keys: 
    44  
     68   
    4569    key_iomput 
    4670    key_mpp_mpi (if you want to run with multiple processes and/or use "detached mode" for the IOs system XIOS) 
     
    4872 
    4973Setup your architecture configuration file 
     74========================================== 
    5075 
    5176All compiler options in NEMO are controlled using files in NEMOGCM/ARCH/arch-'my_arch'.fcm where 'my_arch' is the name of the computing architecture. 
     
    5883 
    5984Compile and create NEMO executable 
     85================================== 
    6086 
    6187The 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. 
    6288As an example, compile GYRE with 'my_arch' to create a 'MY_GYRE' configuration: 
    6389 
    64    cd NEMOGCM/CONFIG; ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' 
     90.. code-block:: sh 
     91 
     92   ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' 
    6593 
    6694The 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). 
    6795 
    68     
     96+------------+----------------------------------------------------+ 
     97| Folder     | Purpose                                            | 
     98+============+====================================================+ 
     99| ``BLD``    |                                                    | 
     100+------------+----------------------------------------------------+ 
     101| ``EXP00``  |                                                    | 
     102+------------+----------------------------------------------------+ 
     103| ``EXPREF`` |                                                    | 
     104+------------+----------------------------------------------------+ 
     105| ``MY_SRC`` |                                                    | 
     106+------------+----------------------------------------------------+ 
     107| ``WORK``   |                                                    | 
     108+------------+----------------------------------------------------+ 
    69109 
    70     WORK 
    71  
    72     
    73  
    74     Folder with the symbolic links to all unpreprocessed routines considered in the configuration 
    75  
    76     BLD 
    77  
    78     
    79  
    80     Compilation folder (executables, headers files, libraries, preprocessed routines, flags, …) 
    81  
    82     EXP00 
    83  
    84     
    85  
    86     Computation folder for running the model (namelists, xml, executables and inputs-outputs) 
    87  
    88     MY_SRC 
    89  
    90     
    91  
    92     Folder intended to contain your customized routines (modified from initial ones or new entire routines) 
     110Folder with the symbolic links to all unpreprocessed routines considered in the configuration 
     111Compilation folder (executables, headers files, libraries, preprocessed routines, flags, …) 
     112Computation folder for running the model (namelists, xml, executables and inputs-outputs) 
     113Folder intended to contain your customised routines (modified from initial ones or new entire routines) 
    93114 
    94115After 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). 
    95116More options 
    96117 
    97         echo "Usage      : "${b_n} \ 
    98             " [-h] [-n name] [-m arch] [-d "dir1 dir2"] [-r conf] [-u conf] [-s Path] [-e Path] [-j No] [-v No] [-k 0/1]"; 
    99         echo " -h               : help"; 
    100         echo " -h institute : specific help for consortium members"; 
    101         echo " -n name      : config name, [-n help] to list existing configurations"; 
    102         echo " -m arch      : choose compiler, [-m help] to list existing compilers"; 
    103         echo " -d dir       : choose NEMO sub-directories"; 
    104         echo " -r conf      : choose reference configuration"; 
    105         echo " -u conf      : choose an unsupported (external) configuration"; 
    106         echo " -s Path      : choose alternative location for NEMO main directory"; 
    107         echo " -e Path      : choose alternative location for MY_SRC directory"; 
    108         echo " -j No        : number of processes used to compile (0=nocompilation)"; 
    109         echo " -v No        : set verbosity level for compilation [0-3]"; 
    110         echo " -k 0/1       : used cpp keys check (default = 1 -> check activated)"; 
    111         echo " -t dir       : temporary directory for compilation" 
    112         echo ""; 
     118.. includefile:: 
    113119 
     120    
     121 
     122----------------- 
    114123Default behaviour 
     124----------------- 
    115125 
    116126    At the first use, you need the -m option to specify the architecture configuration file (compiler and its options, routines and libraries to include), then for next compilation, it is assumed you will be using the same compiler. 
    117127    If –n option is not specified, ORCA2_LIM is the default configuration used.  
    118128 
     129----------------------------- 
    119130Tools used during the process 
     131----------------------------- 
    120132 
    121133    functions.sh : bash functions used by makenemo, for instance to create the WORK directory 
     
    123135    bld.cfg : FCM rules to compile  
    124136 
     137-------- 
    125138Examples 
     139-------- 
    126140 
    127141        echo "Example to install a new configuration MY_CONFIG"; 
     
    148162        echo "./makenemo -n MY_CONFIG -j0 add_key \"key_iomput key_mpp_mpi\" del_key \"key_agrif\" "; 
    149163 
     164----------------- 
    150165Running the model 
     166----------------- 
    151167 
    152168Once makenemo has run successfully, the opa executable is available in CONFIG/"MY_CONFIG"/EXP00 
     
    156172   mpirun -n $NPROCS ./opa    # $NPROCS is the number of processes ; mpirun is your MPI wrapper 
    157173 
     174-------------------------------------------- 
    158175Viewing and changing list of active CPP keys 
     176-------------------------------------------- 
    159177 
    160 For a given configuration (here called MY_CONFIG), the list of active CPP keys can be found in 
     178For a given configuration (here called MY_CONFIG), the list of active CPP keys can be found in:: 
    161179 
    162    NEMOGCM/CONFIG/'MYCONFIG'/cpp_'MY_CONFIG'.fcm 
     180   NEMOGCM/CONFIG/'MYCONFIG'/cpp_'MY_CONFIG'.fcm 
    163181 
    164182This 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. 
     183 
     184.. _HDF5:   http://www.hdfgroup.org/downloads/hdf5 
     185.. _NetCDF: http://www.unidata.ucar.edu/downloads/netcdf 
  • NEMO/trunk/README.rst

    r9650 r10187  
    11.. role:: rstblue 
     2.. role:: rstgreen 
    23.. role:: rstgrey 
    3 .. role:: rstgreen 
     4.. role:: rstgreysup(sup) 
    45 
    5 ================ 
    6 NEMO Ocean Model 
    7 ================ 
    8  
    9 NEMO_ (Nucleus for European Modelling of the Ocean) is a state-of-the-art modelling framework of  
     6NEMO for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework of  
    107ocean related engines for oceanographic research, operational oceanography, seasonal forecast and  
    118[paleo]climate studies. 
    129 
    13 The NEMO ocean model has 3 major components: 
     10Overview 
     11======== 
     12 
     13Distributed under CeCILL license (GNU GPL compatible - see ``./LICENSE``), 
     14the NEMO ocean model has 3 major components: 
    1415 
    1516- :rstblue:`OPA` is fundamental to all users by modelling the ocean [thermo]dynamics and  
    16   solving the primitive equations; 
    17 - :rstgrey:`LIM` for sea-ice simulates ice [thermo]dynamics, brine inclusions and  
    18   subgrid-scale thickness variations; 
    19 - :rstgreen:`TOP-PISCES` models biogeochemistry with TOP for  
    20   the on/offline oceanic tracers transport and PISCES for the biogeochemical processes. 
     17  solving the primitive equations         (``./src/OCE``);  
     18- :rstgrey:`SI`\ :rstgreysup:`3` for sea-ice simulates ice [thermo]dynamics, brine inclusions and  
     19  subgrid-scale thickness variations      (``./src/ICE``);  
     20- :rstgreen:`TOP-PISCES` models biogeochemistry with TOP for the on/offline oceanic tracers transport and  
     21  PISCES for the biogeochemical processes (``./src/MBG``). 
    2122 
    22 These physical engines are described in their respective `reference publications`_. 
     23These physical engines are described in their respective reference publications that must be cited for  
     24any work related to their use. 
    2325 
    24 They are complemented by a 2-way nesting software (AGRIF_) and  
    25 a versatile data assimilation interface with 3 different modules 
    26 (linear-tangent TAM, observational operators OBS, and increment ASM). 
     26Applications and capabilities 
     27============================= 
    2728 
    28 ------------ 
    29 Applications 
    30 ------------ 
     29Not only does the NEMO framework model the ocean circulation, 
     30it offers various features to enable 
    3131 
    32 | Distributed under CeCILL license (GNU GPL compatible - see ``LICENSE``),  
    33   the framework offers several builtins reference configurations to  
    34   check your computing architecture and evaluate the model skills and performances (``./cfgs``). 
    35 | The end user could also find some idealized test cases on the web to serve as examples and  
    36   to study particular processes. 
     32- 2-way nesting package `AGRIF`_ to create embedded zooms seamlessly 
     33- Flexible biogeomchemistry with online coarsening and possible integration of a customized model  
     34- Versatile data assimilation interface with 3 different modules 
     35  (tangent linear, observational operators and increments) 
    3736 
    38 A set of tools is also provided to setup your own configuration and  
    39 [pre|post]process your data (``./tools``). 
     37lation a efficient XIOS_ server for outputing diagnostics a coupled via OASIS_ to alternative components or other models to enable Earth system modelling. 
    4038 
    41 ------- 
    42 Options 
    43 ------- 
     39| Several builtins configurations are provided to assess the skills and performances of the model which 
     40   can be used as templates for setting up a new configuration (``./cfgs``). 
     41| The end user could also find some idealised test cases on the web to serve as examples and 
     42   to study particular processes (``./tests``). 
    4443 
    45 For writing diagnostics in a efficient way, NEMO make use of XIOS_ server which  
    46 controlled the outputs using XML input file. 
     44A set of tools is also provided to setup your own configuration and [pre|post]process your data (``./tools``). 
    4745 
    48 To enable Earth system modelling, NEMO can be interfaced via  
    49 OASIS_ coupleur to external components such as atmospheric models or  
    50 alternative models of sea-ice or biogeochemistry. 
     46Literature 
     47========== 
    5148 
    52 ------------- 
    53 Documentation 
    54 ------------- 
     49| The NEMO reference manual and a quick start guide can be generated from Latex and RST source code files 
     50   (``./doc``), either in PDF or in HTML format, but it might require some additional installations. 
     51| In any case, both formats are available online: `HTML`_ | `PDF`_ 
    5552 
    56 The NEMO reference manual can be generated from the LaTeX source code (``./doc``),  
    57 either in PDF or in HTML format, but it mights require some additionnal installations. 
     53| Since 2014 the project has a `Special Issue`_ in the Geoscientific Model Development (GMD) open-access journal 
     54   from the European Geosciences Union (EGU). 
     55   The main scope is to collect relevant manuscripts which cover a wide variety of topics like 
     56   process studies, new parameterizations, implementation of new model features and new NEMO configurations. 
     57| Also it provides a single portal to search, discover and understand about 
     58   the NEMO modelling framework potential and evolution and to submit their contributions.  
    5859 
    59 In any case, both formats are available online on the `NEMO website`__. 
    60  
    61 --------------------- 
    6260Community development 
    63 --------------------- 
     61===================== 
    6462 
    6563| The NEMO Consortium gathering 6 European institutes organises the sustainable development in order to  
    66   keep a reliable evolving system since 2008. 
    67 | It defined the multiyear development strategy which is implemented by the NEMO System Team. 
     64   keep a reliable evolving system since 2008. 
     65| It defines the multi-year development strategy which is implemented by the NEMO System Team. 
    6866 
    69 -------- 
    70 Acronyms 
    71 -------- 
     67`Working groups`_ are regularly created or resumed to gather the expertise in the NEMO community in order to  
     68focus the development work on a specific subject or major component of NEMO. 
     69 
     70Definitions 
     71=========== 
    7272 
    7373AGRIF 
    74  Adaptive Grid Refinement In Fortran 
     74   *Adaptive Grid Refinement In Fortran*,  
     75   package for the integration of full adaptive mesh refinement features within  
     76   an existing multidimensional finite difference model 
    7577 
    76 LIM 
    77  Louvain-la-Neuve Ice Model 
     78SI\ :sup:`3`\  
     79   *Sea Ice Integrated Initiative*,  
     80   unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework 
    7881 
    79 OPA 
    80  "Océan PArallélisé" (french) 
     82OASIS 
     83   *Ocean Atmosphere Sea Ice Soil*,  
     84   coupling software to synchronise numerical codes representing different components of the climate system 
    8185 
    8286PISCES 
    83  Pelagic Interactions Scheme for Carbon and Ecosystem Studies 
     87   *Pelagic Interactions Scheme for Carbon and Ecosystem Studies*,  
     88   biogeochemical model simulating marine ecosystems, cycles of carbon and the main nutrients 
    8489 
    8590TAM 
    86  Tangent Adjoint Model 
     91   *Tangent linear and Adjoint Model*,  
     92   tools to analyse and control the NEMO dynamical core for a wide range of applications such as 
     93   sensitivity analysis, parameter estimation, vectors computation or data assimilation. 
    8794 
    8895TOP 
    89  Tracers in Ocean Paradigm 
     96   *Tracers in Ocean Paradigm*,  
     97   on/off-line oceanic tracers transport and biogeochemistry models 
    9098 
    9199XIOS 
    92  XML Input Output Server 
     100   *XML Input Output Server*,  
     101   library dedicated to input/output management of climate code 
    93102 
    94 ---- 
    95  
    96 .. _AGRIF:                  http://agrif.imag.fr 
    97 .. _Forge:                  http://forge.ipsl.jussieu.fr/nemo 
    98 .. _NEMO:                   http://www.nemo-ocean.eu 
    99 .. _OASIS:                  http://verc.enes.org/oasis 
    100 .. _reference publications: http://www.nemo-ocean.eu/bibliography/documentation 
    101 .. _XIOS:                   http://forge.ipsl.jussieu.fr/ioserver 
    102  
    103 .. __:  NEMO_ 
     103.. _AGRIF:          http://agrif.imag.fr 
     104.. _HTML:           http://www.nemo-ocean.eu/doc 
     105.. _NEMO:           http://www.nemo-ocean.eu 
     106.. _OASIS:          http://verc.enes.org/oasis 
     107.. _PDF:            http://www.nemo-ocean.eu/wp-content/uploads/NEMO_book.pdf 
     108.. _Special Issue:  http://www.geosci-model-dev.net/special_issue40.html 
     109.. _Working groups: http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups 
     110.. _XIOS:           http://forge.ipsl.jussieu.fr/ioserver 
  • NEMO/trunk/RELEASE_NOTES.rst

    r10150 r10187  
    1 ================ 
    2 NEMO 4.0 Release 
    3 ================ 
     1====================== 
     2What's new in NEMO 4.0 
     3====================== 
    44 
    55.. contents:: 
    6  
    7 ---------- 
    8 What's new 
    9 ---------- 
    10  
     6   :local: 
     7       
    118Original sea-ice component SI\ :sup:`3`\ 
    129======================================== 
     
    108105- The passive tracers transport component was redesigned toward a modular structure and 
    109106  users can enable each module directly through logical flags in namelist_top (no more Fortran macros!). 
    110 - TOP on-line user documentation is available on NEMO Trac platform (TOP-UserQuickGuide_) 
     107- TOP on-line user documentation is available on NEMO Trac platform (`TOP User Quick Guide`_) 
    111108- TOP currently accounts for the following 5 modules: 
    112109 
     
    130127AGRIF (embedded zooms) 
    131128---------------------- 
     129 
     130The NEMO 4.0 includes new capabilities, configurations and test cases with AGRIF: 
     131 
     132.. role:: underline 
     133   :class: underline 
     134 
     135:underline:`New capabilities from NEMO 3.6 to NEMO 4.0` 
     136 
     137AGRIF is continuously maintained so that it could be activated with all NEMO components (OPA, sea-ice, TOP). 
     138Depending on NEMO version, it is nevertheless not the case so that some options may not be compatible with 
     139the use of online grid refinement. 
     140Check out the table below to know the status according to the NEMO release you may use. 
     141 
     142:underline:`Status of available options with AGRIF (if not listed, option is compatible with AGRIF)`: 
     143 
     144+--------------------------------------------------------+----------------+---------------------+ 
     145|                                                        | NEMO 3.6       | NEMO 4.0            | 
     146+========================================================+================+=====================+ 
     147| LIM2                                                   | yes            | ``-``               | 
     148+--------------------------------------------------------+----------------+---------------------+ 
     149| LIM3/SI3                                               | no             | yes                 | 
     150+--------------------------------------------------------+----------------+---------------------+ 
     151| TOP                                                    | yes            | yes                 | 
     152+--------------------------------------------------------+----------------+---------------------+ 
     153| GLS vertical mixing                                    | no             | yes                 | 
     154+--------------------------------------------------------+----------------+---------------------+ 
     155| z*                                                     | no             | yes                 | 
     156+--------------------------------------------------------+----------------+---------------------+ 
     157| z~                                                     | no             | no                  | 
     158+--------------------------------------------------------+----------------+---------------------+ 
     159| Lagrangian icebergs                                    | no             | no                  | 
     160+--------------------------------------------------------+----------------+---------------------+ 
     161| East-west periodic and/or north fold bcs in zooms      | no             | no                  | 
     162+--------------------------------------------------------+----------------+---------------------+ 
     163| Online timing                                          | no             | no                  | 
     164+--------------------------------------------------------+----------------+---------------------+ 
     165| Stochastic parameterization                            | no             | no                  | 
     166+--------------------------------------------------------+----------------+---------------------+ 
     167| Vertical coordinate change in zooms (``key_vertical``) | no             | yes, but not tested | 
     168+--------------------------------------------------------+----------------+---------------------+ 
     169| Number of ghost cells                                  | 1 (hard coded) | 3 (parameter)       | 
     170+--------------------------------------------------------+----------------+---------------------+ 
     171 
     172[Important notice concerning the change of ghost cells number] 
     173 
     174The default number of ghost cells (i.e. the number of cells that serve as open boundary data provision) has been 
     175increased from 1 to 3 in NEMO 4.0. 
     176This allows to properly handle boundary conditions for numerical schemes that 
     177have a discretization order greater than 2. 
     178On the user point of view this does not change anything++ except in the definition of level 1 grids in 
     179the ``AGRIF_FixedGrids.in`` file. 
     180In order to retrieve exactly the position of a nested grid in NEMO 4.0 one has to shift indices by 
     1812 points to the south-west. 
     182Taking the ``ICEDYN`` example above for NEMO 4.0, the "old" NEMO 3.6 corresponding file would contain:: 
     183 
     184   1 
     185   36 65 36 65 3 3 3 
     186   0 
     187 
     188++ Child grid output files are now greater by 4 points in each direction. 
    132189 
    133190- Now compatible with new sea ice component and z* coordinate 
     
    159216- Wave coupling: large scale wave interaction process added in momentum and tracer equations 
    160217- Remove the acceleration of convergence 
    161    
     218 
    162219Numerics 
    163220-------- 
     
    197254 
    198255.. _sea ice working group:       http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/SI3 
    199 .. _TOP-UserQuickGuide:          http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/top-dg/TOP-UserQuickGuide 
     256.. _TOP User Quick Guide:        http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/top-dg/TOP-UserQuickGuide 
    200257 
    201258.. _Hunter 2006:                 http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf 
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