Changeset 10187
- Timestamp:
- 2018-10-09T19:08:59+02:00 (6 years ago)
- Location:
- NEMO/trunk
- Files:
-
- 1 added
- 3 edited
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- Unmodified
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NEMO/trunk/INSTALL.rst
r9596 r10187 1 Install the modelling framework (NEMO and XIOS) 1 ===================== 2 Install the framework 3 ===================== 2 4 3 Last edition: 2018-02-14 21:32 CET by nicolasmartin 5 .. contents:: \ 6 :local: 7 8 Dependencies 9 ============ 4 10 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) 16 14 17 Extract the NEMO code 15 But The following dependencies should be from the official repositories of your Linux distribution but 16 you will probably have to compile them from source for enabling parallel I/O support. 18 17 19 Using your account registered here ('my_login' with password) 18 - `HDF5`_ (C library) 19 - `NetCDF`_ (C and Fortran libraries) 20 21 Extract the source code 22 ======================= 23 24 Download the source code 20 25 21 26 .. code:: console 22 svn --username 'mylogin' co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2015/nemo_v3_6_STABLE/NEMOGCM23 27 24 Description of NEMOGCM directory tree 28 $ svn co http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/releases/release-4.0 25 29 26 The image below shows the directory tree: 30 Description of directory tree 31 ============================= 27 32 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 +-----------+---------------------------------------------------------------+ 35 58 36 59 Extract and install XIOS 60 ======================== 37 61 38 62 Diagnostic outputs from NEMO are handled by the third party XIOS library. … … 42 66 43 67 When you compile NEMO you will need to specify the following CPP keys: 44 68 45 69 key_iomput 46 70 key_mpp_mpi (if you want to run with multiple processes and/or use "detached mode" for the IOs system XIOS) … … 48 72 49 73 Setup your architecture configuration file 74 ========================================== 50 75 51 76 All 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. … … 58 83 59 84 Compile and create NEMO executable 85 ================================== 60 86 61 87 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. 62 88 As an example, compile GYRE with 'my_arch' to create a 'MY_GYRE' configuration: 63 89 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' 65 93 66 94 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). 67 95 68 96 +------------+----------------------------------------------------+ 97 | Folder | Purpose | 98 +============+====================================================+ 99 | ``BLD`` | | 100 +------------+----------------------------------------------------+ 101 | ``EXP00`` | | 102 +------------+----------------------------------------------------+ 103 | ``EXPREF`` | | 104 +------------+----------------------------------------------------+ 105 | ``MY_SRC`` | | 106 +------------+----------------------------------------------------+ 107 | ``WORK`` | | 108 +------------+----------------------------------------------------+ 69 109 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) 110 Folder with the symbolic links to all unpreprocessed routines considered in the configuration 111 Compilation folder (executables, headers files, libraries, preprocessed routines, flags, …) 112 Computation folder for running the model (namelists, xml, executables and inputs-outputs) 113 Folder intended to contain your customised routines (modified from initial ones or new entire routines) 93 114 94 115 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). 95 116 More options 96 117 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:: 113 119 120 121 122 ----------------- 114 123 Default behaviour 124 ----------------- 115 125 116 126 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. 117 127 If –n option is not specified, ORCA2_LIM is the default configuration used. 118 128 129 ----------------------------- 119 130 Tools used during the process 131 ----------------------------- 120 132 121 133 functions.sh : bash functions used by makenemo, for instance to create the WORK directory … … 123 135 bld.cfg : FCM rules to compile 124 136 137 -------- 125 138 Examples 139 -------- 126 140 127 141 echo "Example to install a new configuration MY_CONFIG"; … … 148 162 echo "./makenemo -n MY_CONFIG -j0 add_key \"key_iomput key_mpp_mpi\" del_key \"key_agrif\" "; 149 163 164 ----------------- 150 165 Running the model 166 ----------------- 151 167 152 168 Once makenemo has run successfully, the opa executable is available in CONFIG/"MY_CONFIG"/EXP00 … … 156 172 mpirun -n $NPROCS ./opa # $NPROCS is the number of processes ; mpirun is your MPI wrapper 157 173 174 -------------------------------------------- 158 175 Viewing and changing list of active CPP keys 176 -------------------------------------------- 159 177 160 For a given configuration (here called MY_CONFIG), the list of active CPP keys can be found in 178 For a given configuration (here called MY_CONFIG), the list of active CPP keys can be found in:: 161 179 162 180 NEMOGCM/CONFIG/'MYCONFIG'/cpp_'MY_CONFIG'.fcm 163 181 164 182 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. 183 184 .. _HDF5: http://www.hdfgroup.org/downloads/hdf5 185 .. _NetCDF: http://www.unidata.ucar.edu/downloads/netcdf -
NEMO/trunk/README.rst
r9650 r10187 1 1 .. role:: rstblue 2 .. role:: rstgreen 2 3 .. role:: rstgrey 3 .. role:: rstgre en4 .. role:: rstgreysup(sup) 4 5 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 6 NEMO for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework of 10 7 ocean related engines for oceanographic research, operational oceanography, seasonal forecast and 11 8 [paleo]climate studies. 12 9 13 The NEMO ocean model has 3 major components: 10 Overview 11 ======== 12 13 Distributed under CeCILL license (GNU GPL compatible - see ``./LICENSE``), 14 the NEMO ocean model has 3 major components: 14 15 15 16 - :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 and18 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``). 21 22 22 These physical engines are described in their respective `reference publications`_. 23 These physical engines are described in their respective reference publications that must be cited for 24 any work related to their use. 23 25 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). 26 Applications and capabilities 27 ============================= 27 28 28 ------------ 29 Applications 30 ------------ 29 Not only does the NEMO framework model the ocean circulation, 30 it offers various features to enable 31 31 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) 37 36 38 A set of tools is also provided to setup your own configuration and 39 [pre|post]process your data (``./tools``). 37 lation a efficient XIOS_ server for outputing diagnostics a coupled via OASIS_ to alternative components or other models to enable Earth system modelling. 40 38 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``). 44 43 45 For writing diagnostics in a efficient way, NEMO make use of XIOS_ server which 46 controlled the outputs using XML input file. 44 A set of tools is also provided to setup your own configuration and [pre|post]process your data (``./tools``). 47 45 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. 46 Literature 47 ========== 51 48 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`_ 55 52 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. 58 59 59 In any case, both formats are available online on the `NEMO website`__.60 61 ---------------------62 60 Community development 63 --------------------- 61 ===================== 64 62 65 63 | The NEMO Consortium gathering 6 European institutes organises the sustainable development in order to 66 67 | It define d 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. 68 66 69 -------- 70 Acronyms 71 -------- 67 `Working groups`_ are regularly created or resumed to gather the expertise in the NEMO community in order to 68 focus the development work on a specific subject or major component of NEMO. 69 70 Definitions 71 =========== 72 72 73 73 AGRIF 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 75 77 76 LIM 77 Louvain-la-Neuve Ice Model 78 SI\ :sup:`3`\ 79 *Sea Ice Integrated Initiative*, 80 unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework 78 81 79 OPA 80 "Océan PArallélisé" (french) 82 OASIS 83 *Ocean Atmosphere Sea Ice Soil*, 84 coupling software to synchronise numerical codes representing different components of the climate system 81 85 82 86 PISCES 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 84 89 85 90 TAM 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. 87 94 88 95 TOP 89 Tracers in Ocean Paradigm 96 *Tracers in Ocean Paradigm*, 97 on/off-line oceanic tracers transport and biogeochemistry models 90 98 91 99 XIOS 92 XML Input Output Server 100 *XML Input Output Server*, 101 library dedicated to input/output management of climate code 93 102 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 ====================== 2 What's new in NEMO 4.0 3 ====================== 4 4 5 5 .. contents:: 6 7 ---------- 8 What's new 9 ---------- 10 6 :local: 7 11 8 Original sea-ice component SI\ :sup:`3`\ 12 9 ======================================== … … 108 105 - The passive tracers transport component was redesigned toward a modular structure and 109 106 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`_) 111 108 - TOP currently accounts for the following 5 modules: 112 109 … … 130 127 AGRIF (embedded zooms) 131 128 ---------------------- 129 130 The 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` 136 137 AGRIF is continuously maintained so that it could be activated with all NEMO components (OPA, sea-ice, TOP). 138 Depending on NEMO version, it is nevertheless not the case so that some options may not be compatible with 139 the use of online grid refinement. 140 Check 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] 173 174 The default number of ghost cells (i.e. the number of cells that serve as open boundary data provision) has been 175 increased from 1 to 3 in NEMO 4.0. 176 This allows to properly handle boundary conditions for numerical schemes that 177 have a discretization order greater than 2. 178 On the user point of view this does not change anything++ except in the definition of level 1 grids in 179 the ``AGRIF_FixedGrids.in`` file. 180 In order to retrieve exactly the position of a nested grid in NEMO 4.0 one has to shift indices by 181 2 points to the south-west. 182 Taking 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. 132 189 133 190 - Now compatible with new sea ice component and z* coordinate … … 159 216 - Wave coupling: large scale wave interaction process added in momentum and tracer equations 160 217 - Remove the acceleration of convergence 161 218 162 219 Numerics 163 220 -------- … … 197 254 198 255 .. _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-UserQuickGuide256 .. _TOP User Quick Guide: http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/top-dg/TOP-UserQuickGuide 200 257 201 258 .. _Hunter 2006: http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf
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