Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found

Target

Select target project
No results found
Show changes
Commits on Source (295)
Hide whitespace changes
Inline Side-by-side
Showing
with 238 additions and 579 deletions
.gitlab/issue_templates/Bug.md 0 → 100644
View file @ 4a9f4b18
#### Context
_Please provide informations on how to reproduce the bug:_
- [x] Branches impacted: current release and/or main
- [x] Reference configuration/test case (chosen or used as template) ~AMM ~gyre ~orca ~papa or engines involved ~ABL ~NST ~OFF ~TOP ~SAO ~SAS ~"SI³" ~SWE
- [x] Computing architecture: compiler, MPI & NetCDF libs (name and version)
- [x] Dependencies: ~AGRIF ~BFM ~CICE ~OASIS ~XIOS (with known branch and hash/revision/version), ...
- [ ] _Any other relevant information_
#### Analysis
_Please give your thoughts on the issue._
#### Fix
_Please share your proven solution or your recommendation on how to proceed._
---
_You can_
- :clipboard: _Copy code blocks_ (\`\`\`fortran ...\`\`\`) _or diff outputs_ (\`\`\`diff ...\`\`\`)
- :paperclip: _Include files_
- :link: _Add external links._
:warning: _Please remove all unnecessary lines in this description, like the one you are reading in italic, before creating the issue._ :warning:
.gitlab/issue_templates/Feature.md 0 → 100644
View file @ 4a9f4b18
#### Context
_Please provide informations on how to set the modelling environment_
- [ ] Reference configuration/test case (to add, chosen or used as template)
- [x] Modifications of versioned files: Fortran routines (`*.[Ffh]90`), namelists (`namelist\_*cfg`), outputs settings (`*.xml`), ...
- [ ] Additional dependencies
- [ ] New datasets
- [ ] _Any other relevant information_
#### Proposal
_Please share your ideas or your wishes about modelling improvements for the NEMO model._
_In particular, express if you are willing to contribute personally to the implementation of this feature in NEMO._
---
_You can_
- :clipboard: _Copy code blocks_ (\`\`\`fortran ...\`\`\`) _or diff outputs_ (\`\`\`diff ...\`\`\`)
- :paperclip: _Include files_
- :link: _Add external links._
:warning: _Please remove all unnecessary lines in this description, like the one you are reading in italic, before creating the issue._ :warning:
.gitlab/issue_templates/Task_preview.md 0 → 100644
View file @ 4a9f4b18
#### Development description
_Describe the goal and the methodology._
_Add reference documents or publications if relevant._
#### Code implementation
_Describe flow chart of the changes in the code._
_List the Fortran modules and subroutines to be created/edited/deleted._
_Detailed list of new variables to be defined (including namelists), give for each the chosen name and description wrt coding rules._
#### Documentation updates
_Using previous parts, define the main changes to be done in the ~doc (manuals, guide, web pages, ...)._
.gitlab/merge_request_templates/.gitkeep 0 → 100644
View file @ 4a9f4b18
.gitlab/merge_request_templates/Task_review.md 0 → 100644
View file @ 4a9f4b18
#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and reproducibility for each of the reference configuration) and detailed results of restartability and reproducibility when the option is activated on specified configurations used for this test.
**Regular checks**
- [ ] Can this change be shown to produce expected impact (option activated)?
- [ ] Can this change be shown to have a null impact (option not activated)?
- [ ] Results of the required bit comparability tests been run: are there no differences when activating the development?
- [ ] If some differences appear, is reason for the change valid/understood?
- [ ] If some differences appear, is the impact as expected on model configurations?
- [ ] Is this change expected to preserve all diagnostics?
- [ ] If no, is reason for the change valid/understood?
- [ ] Are there significant changes in run time/memory?
#### Review
A successful review is needed to schedule the merge of this development into the future NEMO release during next Merge Party (usually in November).
**Assessments**
- [ ] Is the proposed methodology now implemented?
- [ ] Are the code changes in agreement with the flowchart defined at preview step?
- [ ] Are the code changes in agreement with list of routines and variables as proposed at preview step?
- [ ] If, not, are the discrepancies acceptable?
- [ ] Is the in-line documentation accurate and sufficient?
- [ ] Do the code changes comply with NEMO coding standards?
- [ ] Is the development documented with sufficient details for others to understand the impact of the change?
- [ ] Is the project ~doc (manual, guide, web, ...) now updated or completed following the proposed summary in preview section?
CHANGES.md deleted 100644 → 0
View file @ 2095f237
# List of the main additions of the new 4.2 release - February 2022
This section provides you an overview of the major NEMO upgrades as included in the new 4.2 release.
It includes instructions on how to move to new version and a list of the novelties of changed NEMO modules.
If you are willing to port an existing configuration in order to start using this new release, it is sugggested to also look at the 4.2 [Migration Guide](https://sites.nemo-ocean.io/user-guide/migration.html).
## KERNEL
- Quasi Eulerian Coordinates
- New HPG schemes (improvements and new option)
- Preparatory stages for new RK3 time stepping scheme (includes time-pointer changes, DO LOOP macros, changes in main arrays dimensions)
- Full Shallow Water setup
- New vertical scale factors management in time reducing meùory footprint : added key qco (Quasi Eulerian Coordinates), key linssh, see Migration Guide
## AIR SEA INTERACTIONS
- Currents feedbacks
- Mass-flux convection scheme (still not compatible with TOP & PISCES)
- Bulk improvements
- Atmospheric Boundary layer model (1D vertical as for now) & tools improvements
- Wave forcing improvements
## AGRIF zooms
- Improvement of Agrif for global configurations (periodic, north fold zoom, HPC),
- Allow AGRIF for multiple vertical grids
- Updated Nesting Tools to set up the AGRIF zooms
## Sea-ice SI3
- EAP & VP rheology (V&V to complete)
- Melt ponds (preliminary implementation)
- Updated Reference Manual will be made available to users by March 2022
## ENHANCEMENTS
- Ocean column properties in NEMO-ICB
- OSMOSIS
- Update internal tidal mixing
## Tracers and biogeochemistry TOP
- Ice sheet iron sources
- Scheme for vertical penetration of visible light
## DATA interface
- OBS modifications
## Input Output Manager
- Use XIOS to read & write restart file (allowing to produce a unique restart file while using domain decomposition)
## High Performance Computing HPC
- MPI Communication cleanup & improvements using MPI3
- Reduce memory footprint
- Improved computational performance of solar penetration scheme
So as some new features implemented, and now needing further work to produce actual performance improvements:
- Extra Halo extension
- Mixed precision preparatory phase
- Loop fusion
- Tiling
## VERIFICATION & VALIDATION
- Tests cases now available with most new developments
- SETTE validation script improvements
- OASIS test case for ocean atmosphere coupled interface
CONTRIBUTING.rst deleted 100644 → 0
View file @ 2095f237
************
Contributing
************
.. todo::
.. contents::
:local:
Sending feedbacks
=================
| Sending feedbacks is a useful way to contribute to NEMO efficency and reliability. Before doing so,
please check here :forge:`search <search on the developement platform>` in wiki, tickets, forum and online
documentation if the subject has already been discussed. You can either contribute to an existing
discussion, or
| Create an entry for the discussion online, according to your needs
- You have a question: create a topic in the appropriate :forge:`discussion <forum>`
- You would like to raise and issue: open a new ticket of the right type depending of its severity
- "Unavoidable" :forge:`newticket?type=Bug <bug>`
- "Workable" :forge:`newticket?type=Defect <defect>`
Please follow the guidelines and try to be as specific as possible in the ticket description.
New development
===============
You have build a development relevant for NEMO shared reference: an addition of the source code,
a full fork of the reference, ...
You may want to share it with the community (see Hack below) or to propose it for implementation in the future
NEMO release (see Proposal / Task below).
The proposals for developments to be included in the shared NEMO reference are first examined by NEMO Developers
Committee / Scientific Advisory Board.
The implementation of a new development requires some additionnal work from the intial developer.
These tasks will need to be scheduled with NEMO System Team.
Hack
----
You only would like to inform NEMO community about your developments.
You can promote your work on NEMO forum gathering the contributions fromof the community by creating
a specific topic here :forge:`discussion/forum/5 <dedicated forum>`
Proposal / Task
---------------
| Your development is quite small, and you would only like to offer it as a possible enhancement. Please suggest it
as an enhancement here :forge:`newticket?type=Enhancement <enhancement>` . It will be taken in account, if
feasible, by NEMO System Team. To ease the process, it is suggested, rather than attaching the modified
routines to the ticket, to highlight the proposed changes by adding to the ticket the output of ``svn diff``
or ``svn patch`` from your working copy.
| Your development seems relevant for addition into the future release of NEMO shared reference.
Implementing it into NEMO shared reference following the usual quality control will require some additionnal work
from you and also from the NEMO System Team in charge of NEMO development. In order to evaluate the work,
your suggestion should be send as a proposed enhancement here :forge:`newticket?type=Enhancement <enhancement>`
including description of the development, its implementation, and the existing validations.
The proposed enhancement will be examined by NEMO Developers Committee / Scientific Advisory Board.
Once approved by the Committee, the assicated development task can be scheduled in NEMO development work plan,
and tasks distributed between you as initial developer and PI of this development action, and the NEMO System Team.
Once sucessful (meeting the usual quality control steps) this action will allow the merge of these developments with
other developments of the year, building the future NEMO.
INSTALL.rst deleted 100644 → 0
View file @ 2095f237
*******************
Build the framework
*******************
.. todo::
TBD
.. contents::
:local:
Prerequisites
=============
| The NEMO source code is written in *Fortran 95* and
some of its prerequisite tools and libraries are already included in the download.
| It contains the AGRIF_ preprocessing program ``conv``; the FCM_ build system and
the IOIPSL_ library for parts of the output.
System dependencies
-------------------
In the first place the other requirements should be provided natively by your system or
can be installed from the official repositories of your Unix-like distribution:
- *Perl* interpreter
- *Fortran* compiler (``ifort``, ``gfortran``, ``pgfortran``, ...),
- *Message Passing Interface (MPI)* implementation (e.g. |OpenMPI|_ or |MPICH|_).
- |NetCDF|_ library with its underlying |HDF|_
**NEMO, by default, takes advantage of some MPI features introduced into the MPI-3 standard.**
.. hint::
The MPI implementation is not strictly essential
since it is possible to compile and run NEMO on a single processor.
However most realistic configurations will require the parallel capabilities of NEMO and
these use the MPI standard.
.. note::
On older systems, that do not support MPI-3 features,
the ``key_mpi2`` preprocessor key should be used at compile time.
This will limit MPI features to those defined within the MPI-2 standard
(but will lose some performance benefits).
.. |OpenMPI| replace:: *OpenMPI*
.. _OpenMPI: https://www.open-mpi.org
.. |MPICH| replace:: *MPICH*
.. _MPICH: https://www.mpich.org
.. |NetCDF| replace:: *Network Common Data Form (NetCDF)*
.. _NetCDF: https://www.unidata.ucar.edu
.. |HDF| replace:: *Hierarchical Data Form (HDF)*
.. _HDF: https://www.hdfgroup.org
Specifics for NetCDF and HDF
----------------------------
NetCDF and HDF versions from official repositories may have not been compiled with MPI support.
However access to all the options available with the XIOS IO-server will require
the parallelism of these libraries.
| **To satisfy these requirements, it is common to have to compile from source
in this order HDF (C library) then NetCDF (C and Fortran libraries)**
| It is also necessary to compile these libraries with the same version of the MPI implementation that
both NEMO and XIOS (see below) have been compiled and linked with.
.. hint::
| It is difficult to define the options for the compilation as
they differ from one architecture to another according to
the hardware used and the software installed.
| The following is provided without any warranty
.. code-block:: console
$ ./configure [--{enable-fortran,disable-shared,enable-parallel}] ...
It is recommended to build the tests ``--enable-parallel-tests`` and run them with ``make check``
Particular versions of these libraries may have their own restrictions.
State the following requirements for netCDF-4 support:
.. caution::
| When building NetCDF-C library versions older than 4.4.1, use only HDF5 1.8.x versions.
| Combining older NetCDF-C versions with newer HDF5 1.10 versions will create superblock 3 files
that are not readable by lots of older software.
Extract and install XIOS
========================
With the sole exception of running NEMO in mono-processor mode
(in which case output options are limited to those supported by the ``IOIPSL`` library),
diagnostic outputs from NEMO are handled by the third party ``XIOS`` library.
It can be used in two different modes:
:*attached*: Every NEMO process also acts as a XIOS server
:*detached*: Every NEMO process runs as a XIOS client.
Output is collected and collated by external, stand-alone XIOS server processors.
Instructions on how to install XIOS can be found on its :xios:`wiki<>`.
.. hint::
It is recommended to use XIOS 2.5 release.
This version should be more stable (in terms of future code changes) than the XIOS trunk.
It is also the one used by the NEMO system team when testing all developments and new releases.
This particular version has its own branch and can be checked out with:
.. code:: console
$ svn co https://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5
Download and install the NEMO code
==================================
Checkout the NEMO sources
-------------------------
.. code:: console
$ svn co https://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk
Description of 1\ :sup:`st` level tree structure
------------------------------------------------
+---------------+----------------------------------------+
| :file:`arch` | Compilation settings |
+---------------+----------------------------------------+
| :file:`cfgs` | :doc:`Reference configurations <cfgs>` |
+---------------+----------------------------------------+
| :file:`doc` | :doc:`Documentation <doc>` |
+---------------+----------------------------------------+
| :file:`ext` | Dependencies included |
| | (``AGRIF``, ``FCM`` & ``IOIPSL``) |
+---------------+----------------------------------------+
| :file:`mk` | Compilation scripts |
+---------------+----------------------------------------+
| :file:`src` | :doc:`Modelling routines <src>` |
+---------------+----------------------------------------+
| :file:`tests` | :doc:`Test cases <tests>` |
| | (unsupported) |
+---------------+----------------------------------------+
| :file:`tools` | :doc:`Utilities <tools>` |
| | to {pre,post}process data |
+---------------+----------------------------------------+
Setup your architecture configuration file
------------------------------------------
All compiler options in NEMO are controlled using files in :file:`./arch/arch-'my_arch'.fcm` where
``my_arch`` is the name of the computing architecture
(generally following the pattern ``HPCC-compiler`` or ``OS-compiler``).
It is recommended to copy and rename an configuration file from an architecture similar to your owns.
You will need to set appropriate values for all of the variables in the file.
In particular the FCM variables:
``%NCDF_HOME``; ``%HDF5_HOME`` and ``%XIOS_HOME`` should be set to
the installation directories used for XIOS installation
.. code-block:: sh
%NCDF_HOME /usr/local/path/to/netcdf
%HDF5_HOME /usr/local/path/to/hdf5
%XIOS_HOME /home/$( whoami )/path/to/xios-2.5
%OASIS_HOME /home/$( whoami )/path/to/oasis
Create and compile a new configuration
======================================
The main script to {re}compile and create executable is called :file:`makenemo` located at
the root of the working copy.
It is used to identify the routines you need from the source code, to build the makefile and run it.
As an example, compile a :file:`MY_GYRE` configuration from GYRE with 'my_arch':
.. code-block:: sh
./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE'
Then at the end of the configuration compilation,
:file:`MY_GYRE` directory will have the following structure.
+------------+----------------------------------------------------------------------------+
| Directory | Purpose |
+============+============================================================================+
| ``BLD`` | BuiLD folder: target executable, headers, libs, preprocessed routines, ... |
+------------+----------------------------------------------------------------------------+
| ``EXP00`` | Run folder: link to executable, namelists, ``*.xml`` and IOs |
+------------+----------------------------------------------------------------------------+
| ``EXPREF`` | Files under version control only for :doc:`official configurations <cfgs>` |
+------------+----------------------------------------------------------------------------+
| ``MY_SRC`` | New routines or modified copies of NEMO sources |
+------------+----------------------------------------------------------------------------+
| ``WORK`` | Links to all raw routines from :file:`./src` considered |
+------------+----------------------------------------------------------------------------+
After successful execution of :file:`makenemo` command,
the executable called `nemo` is available in the :file:`EXP00` directory
More :file:`makenemo` options
-----------------------------
``makenemo`` has several other options that can control which source files are selected and
the operation of the build process itself.
.. literalinclude:: ../../../makenemo
:language: text
:lines: 119-143
:caption: Output of ``makenemo -h``
These options can be useful for maintaining several code versions with only minor differences but
they should be used sparingly.
Note however the ``-j`` option which should be used more routinely to speed up the build process.
For example:
.. code-block:: sh
./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' -j 8
will compile up to 8 processes simultaneously.
Default behaviour
-----------------
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.
If the ``-n`` option is not specified the last compiled configuration will be used.
Tools used during the process
-----------------------------
* :file:`functions.sh`: bash functions used by ``makenemo``, for instance to create the WORK directory
* :file:`cfg.txt` : text list of configurations and source directories
* :file:`bld.cfg` : FCM rules for compilation
Examples
--------
.. literalinclude:: ../../../makenemo
:language: text
:lines: 146-153
Running the model
=================
Once :file:`makenemo` has run successfully,
the ``nemo`` executable is available in :file:`./cfgs/MY_CONFIG/EXP00`.
For the reference configurations, the :file:`EXP00` folder also contains the initial input files
(namelists, ``*.xml`` files for the IOs, ...).
If the configuration needs other input files, they have to be placed here.
.. code-block:: sh
cd 'MY_CONFIG'/EXP00
mpirun -n $NPROCS ./nemo # $NPROCS is the number of processes
# mpirun is your MPI wrapper
Viewing and changing list of active CPP keys
============================================
For a given configuration (here called ``MY_CONFIG``),
the list of active CPP keys can be found in :file:`./cfgs/'MYCONFIG'/cpp_MY_CONFIG.fcm`
This text file can be edited by hand or with :file:`makenemo` to change the list of active CPP keys.
Once changed, one needs to recompile ``nemo`` in order for this change to be taken in account.
Note that most NEMO configurations will need to specify the following CPP keys:
``key_xios`` for IOs. MPI parallelism is activated by default. Use ``key_mpi_off`` to compile without MPI.
README.rst
View file @ 4a9f4b18
.. todo::
.. contents::
:local:
NEMO
====
Welcome to NEMO home page!
==========================
NEMO_ for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework for
research activities and forecasting services in ocean and climate sciences,
*Nucleus for European Modelling of the Ocean* (NEMO) is a state-of-the-art modelling
framework for research activities and forecasting services in ocean and climate sciences,
developed in a sustainable way by the NEMO European consortium since 2008.
This page intends to help to get started using NEMO platform and to orientate users to the different levels of information.
It starts here with NEMO release 4.2.0.
Reminder: [Former web platform forge](https://forge.ipsl.jussieu.fr/nemo) (SVN+Trac) contains previous documentation and releases since the beginning of the project up to of NEMO 4.0.
Getting started
===============
Getting hands on NEMO: first steps are described in detail in the "How to" NEMO users's guide.
Download, build the environment create the executable, and make a first run are described here: https://sites.nemo-ocean.io/user-guide/.
If you are already using NEMO with a previous release, refer to the [Migration Guide] (https://sites.nemo-ocean.io/user-guide/migration.html) to help making the move to 4.2.0.
The above users guides cover in detail what is available from gitlab and supported by NEMO System Team.
Aside from this web platform, the tests cases are also available from https://github.com/NEMO-ocean/NEMO-examples. These tests cases can be useful for studentes, outreach, exploring some specific aspects of NEMO with light configurations... It is also set up in order to gather the tests cases you may have developped and want to share with the community. Feel free to contribute!
A summary on how to get code dependencies, compile and execute NEMO is also available here
(:file:`./INSTALL.rst`).
Project documentation
=====================
Reference manuals fully describing NEMO for the three main component
* |OCE| models the ocean {thermo}dynamics and solves the primitive equations (:file:`./src/OCE`)
* |ICE| simulates sea-ice {thermo}dynamics, brine inclusions and subgrid-scale thickness variations (:file:`./src/ICE`)
* |MBG| models the {on,off}line oceanic tracers transport and biogeochemical processes (:file:`./src/TOP`)
are available from zenodo
============ ============================================== ===============================================
Component Reference Manual (from zenondo, DOI to quote) Reference manual (pdf on line version on gitlab)
============ ============================================== ===============================================
|NEMO-OCE| |https://zenodo.org/record/1464816|
|NEMO-ICE| |https://zenodo.org/record/1471689| *Updated version will be online since Mar 2022*
|NEMO-MBG| |https://zenodo.org/record/1471700|
============ ============================================== ===============================================
These reference manuals are the publications that should be cited in your own publications. Please visit [How to cite?](https://www.nemo-ocean.eu/bibliography/how-to-cite/) for details.
New features of 4.2.0 release are described here (:file:`./CHANGES.md`)
Asking questions, echange information
=====================================
- [Register once for all and use the NEMO forums](https://nemo-ocean.discourse.group) to share and discuss with the NEMO community.
- [Register once for all and receive by mail the NEMO newsletter ](https://listes.ipsl.fr/sympa/subscribe/nemo-newsletter) : recommended for all users to receive the major announcements from the project (new releases, open meetings and main informations). Low traffic: about ten messages a year.
Contributing to NEMO visibility: projects and publications
==========================================================
Please help us justifying the NEMO development efforts by
- Adding your publications using NEMO and its outputs here: https://www.nemo-ocean.eu/bibliography/publications/add
- Describing your project using NEMO here: https://www.nemo-ocean.eu/projects/add
NEMO also has a `Special Issue`_ in the open-access journal
Geoscientific Model Development (GMD) from the European Geosciences Union (https://gmd.copernicus.org/articles/special_issue40.html).
The main scope is to collect relevant manuscripts covering various topics and
to provide a single portal to assess the model potential and evolution.
More on NEMO's features
=======================
Not only does the NEMO framework model the ocean circulation,
it offers various features to enable
- Create :doc:`embedded zooms<zooms>` seamlessly thanks to 2-way nesting package AGRIF_.
- Opportunity to integrate an :doc:`external biogeochemistry model<tracers>`
- Versatile :doc:`data assimilation<da>`
- Generation of :doc:`diagnostics<diags>` through effective XIOS_ system
- Roll-out Earth system modeling with :doc:`coupling interface<cplg>` based on OASIS_
Several :doc:`built-in configurations<cfgs>` are provided to
evaluate the skills and performances of the model which
can be used as templates for setting up a new configurations (:file:`./cfgs`).
The user can also checkout available :doc:`idealized test cases<tests>` that
address specific physical processes (:file:`./tests`).
A set of :doc:`utilities <tools>` is also provided to {pre,post}process your data (:file:`./tools`).
Contributing to NEMO development
================================
For all information please refer to the `NEMO wiki <https://forge.nemo-ocean.eu/nemo/nemo/-/wikis/home>`_
NEMO intends to be written in a way allowing easy plug of developments.
You are also welcome to contribute to the development of the NEMO Shared reference.
NEMO development is driven by NEMO Consortium planning and producing NEMO's sustainable development in order to
keep a reliable evolving framework.
Development is organised and scheduled through a five years development strategy, Working groups and the activities of the development team (named NEMO System Team) in a yearly workplan. [More information here] (https://forge.nemo-ocean.eu/developers/home/-/wikis/Home)
How to cite
===========
To acknowledge the sustainable development efforts of the NEMO Consortium, please quote `these references <https://www.nemo-ocean.eu/bibliography/how-to-cite/>`_ in your publications and presentations using NEMO.
Disclaimer
==========
The NEMO source code is freely available and distributed under
:download:`CeCILL v2.0 license <../../../LICENSE>` (GNU GPL compatible).
`CeCILL v2.0 license <./LICENSE>`_ (GNU GPL compatible).
You can use, modify and/or redistribute the software under its terms,
but users are provided only with a limited warranty and the software's authors and
......
REFERENCES.bib deleted 100644 → 0
View file @ 2095f237
@manual{ NEMO_man,
title = "NEMO ocean engine",
series = "Scientific Notes of Climate Modelling Center",
number = "27",
author = "Gurvan Madec and NEMO System Team",
institution = "Institut Pierre-Simon Laplace (IPSL)",
publisher = "Zenodo",
issn = "1288-1619",
doi = "10.5281/zenodo.1464816"
}
% edition="",
% year=""
@manual{ SI3_man,
title = "Sea Ice modelling Integrated Initiative (SI$^3$) -- The
NEMO sea ice engine",
series = "Scientific Notes of Climate Modelling Center",
number = "31",
author = "NEMO Sea Ice Working Group",
institution = "Institut Pierre-Simon Laplace (IPSL)",
publisher = "Zenodo",
issn = "1288-1619",
doi = "10.5281/zenodo.1471689"
}
% edition="",
% year=""
@manual{ TOP_man,
title = "Tracers in Ocean Paradigm (TOP) -- The NEMO passive
tracers engine",
series = "Scientific Notes of Climate Modelling Center",
number = "28",
author = "NEMO TOP Working Group",
institution = "Institut Pierre-Simon Laplace (IPSL)",
publisher = "Zenodo",
issn = "1288-1619",
doi = "10.5281/zenodo.1471700"
}
% edition="",
% year=""
@article{ TAM_pub,
title = "NEMOTAM: Tangent and Adjoint Models for the ocean
modelling platform NEMO",
pages = "1245--1257",
journal = "Geoscientific Model Development",
volume = "8",
number = "4",
author = "Vidard, A. and Bouttier, P.-A. and Vigilant, F.",
year = "2015",
doi = "10.5194/gmd-8-1245-2015"
}
arch/CMCC/arch-X64_JUNO.env 0 → 100644
View file @ 4a9f4b18
module purge
module load intel-2021.6.0/cmake/3.25.1-7wfsx
module load oneapi-2022.1.0/compiler-rt/2022.1.0
module load intel-2021.6.0/2021.6.0
module load impi-2021.6.0/2021.6.0
module load intel-2021.6.0/impi-2021.6.0/hdf5-threadsafe/1.13.3-zbgha
module load intel-2021.6.0/impi-2021.6.0/netcdf-c-threadsafe/4.9.0-wpe4t
module load intel-2021.6.0/impi-2021.6.0/netcdf-fortran-threadsafe/4.6.0-75oow
module load intel-2021.6.0/impi-2021.6.0/parallel-netcdf/1.12.3-eshb5
module load intel-2021.6.0/perl/5.36.0-jj4hw
module load intel-2021.6.0/perl-uri/1.72-6at2i
module load intel-2021.6.0/impi-2021.6.0/xios/2.5-36kwn
# set linker path to 64-bit libraries
export LD_LIBRARY_PATH="/lib64/":$LD_LIBRARY_PATH
arch/CMCC/arch-X64_JUNO.fcm 0 → 100644
View file @ 4a9f4b18
# mpi ifort compiler options for ZEUS cluster + XIOS
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
#
# CPP Pre-processor
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# FPPFLAGS pre-processing flags
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# AR assembler
# ARFLAGS assembler flags
# MK make (usually GNU make)
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
# Environment variables are set automatically when loading modules on JUNO cluster (see arch-X64_JUNO.env)
%NCDF_INC -I${NETCDF_FORTRAN}/include -I${NETCDF_C}/include -I${PARALLEL_NETCDF}/include
%NCDF_LIB -L${NETCDF_FORTRAN}/lib -lnetcdff -L${NETCDF_C}/lib -lnetcdf -L${PARALLEL_NETCDF}/lib -lpnetcdf
%HDF5_INC -I${HDF5}/include
%HDF5_LIB -L${HDF5}/lib -lhdf5_hl -lhdf5
%XIOS_INC -I${XIOS}/inc
%XIOS_LIB -L${XIOS}/lib -lxios
%USER_INC %XIOS_INC %NCDF_INC %HDF5_INC
%USER_LIB %XIOS_LIB %NCDF_LIB %HDF5_LIB
%FC mpiifort
%FCFLAGS -r8 -O3 -fp-model source -traceback -qmkl=cluster -march=icelake-client -mtune=icelake-client -qopt-zmm-usage=low -no-fma
%FFLAGS %FCFLAGS
%CC mpiicc
%CFLAGS -O0
%LD mpiifort
%LDFLAGS -lstdc++ -lgpfs
%AR ar
%ARFLAGS -r
%CPP icc
%FPPFLAGS -E -P -traditional
%MK gmake
arch/CMCC/arch-X64_JUNO_DEBUG.env 0 → 120000
View file @ 4a9f4b18
arch-X64_JUNO.env
\ No newline at end of file
arch/CMCC/arch-X64_JUNO_DEBUG.fcm 0 → 100644
View file @ 4a9f4b18
# mpi ifort compiler options for ZEUS cluster + XIOS
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
#
# CPP Pre-processor
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# FPPFLAGS pre-processing flags
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# AR assembler
# ARFLAGS assembler flags
# MK make (usually GNU make)
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
# Environment variables are set automatically when loading modules on JUNO cluster (see arch-X64_JUNO.env)
%NCDF_INC -I${NETCDF_FORTRAN}/include -I${NETCDF_C}/include -I${PARALLEL_NETCDF}/include
%NCDF_LIB -L${NETCDF_FORTRAN}/lib -lnetcdff -L${NETCDF_C}/lib -lnetcdf -L${PARALLEL_NETCDF}/lib -lpnetcdf
%HDF5_INC -I${HDF5}/include
%HDF5_LIB -L${HDF5}/lib -lhdf5_hl -lhdf5
%XIOS_INC -I${XIOS}/inc
%XIOS_LIB -L${XIOS}/lib -lxios
%USER_INC %XIOS_INC %NCDF_INC %HDF5_INC
%USER_LIB %XIOS_LIB %NCDF_LIB %HDF5_LIB
%FC mpiifort
%FCFLAGS -r8 -g -O0 -check all -fp-model source -traceback -qmkl=cluster -march=icelake-client -mtune=icelake-client -qopt-zmm-usage=low -no-fma
%FFLAGS %FCFLAGS
%CC mpiicc
%CFLAGS -O0
%LD mpiifort
%LDFLAGS -lstdc++ -lgpfs
%AR ar
%ARFLAGS -r
%CPP icc
%FPPFLAGS -E -P -traditional
%MK gmake
arch/CMCC/arch-X64_ZEUS.fcm
View file @ 4a9f4b18
......@@ -3,8 +3,8 @@
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_iomput is activated)
# XIOS_LIB xios library (taken into accound only if key_iomput is activated)
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
#
# CPP Pre-processor
# FC Fortran compiler command
......
arch/CNRS/arch-X64_IRENE.fcm
View file @ 4a9f4b18
......@@ -30,7 +30,7 @@
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
%XIOS_HOME $CCCWORKDIR/xios-2.5
%XIOS_HOME $CCCWORKDIR/xios-trunk
%OASIS_HOME $CCCWORKDIR/now/models/oa3mct
%NCDF_INC -I$NETCDFFORTRAN_INCDIR -I$NETCDF_INCDIR
......@@ -54,5 +54,5 @@
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC cc
%CC icc
%CFLAGS -O0
arch/CNRS/arch-X64_IRENE_DEBUG.fcm
View file @ 4a9f4b18
......@@ -30,7 +30,7 @@
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
%XIOS_HOME $CCCWORKDIR/xios-2.5
%XIOS_HOME $CCCWORKDIR/xios-trunk
%OASIS_HOME $CCCWORKDIR/now/models/oa3mct
%NCDF_INC -I$NETCDFFORTRAN_INCDIR -I$NETCDF_INCDIR
......@@ -54,5 +54,5 @@
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC cc
%CC icc
%CFLAGS -O0
arch/CNRS/arch-X64_IRENE_GCC.fcm
View file @ 4a9f4b18
......@@ -16,7 +16,7 @@
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
%XIOS_HOME $CCCWORKDIR/xios-2.5_gcc
%XIOS_HOME $CCCWORKDIR/xios-trunk_gcc
%OASIS_HOME $CCCWORKDIR/now/models/oa3mct
%NCDF_INC -I$NETCDFFORTRAN_INCDIR -I$NETCDF_INCDIR
......
arch/CNRS/arch-X64_IRENE_GCC_DEBUG.fcm
View file @ 4a9f4b18
......@@ -16,7 +16,7 @@
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
%XIOS_HOME $CCCWORKDIR/xios-2.5_gcc
%XIOS_HOME $CCCWORKDIR/xios-trunk_gcc
%OASIS_HOME $CCCWORKDIR/now/models/oa3mct
%NCDF_INC -I$NETCDFFORTRAN_INCDIR -I$NETCDF_INCDIR
......
arch/CNRS/arch-X64_JEANZAY.fcm
View file @ 4a9f4b18
......@@ -36,7 +36,7 @@
#---------------------------------------------------------------------------------------------
#
#
%XIOS_HOME $WORK/xios-2.5
%XIOS_HOME $WORK/xios-trunk
%OASIS_HOME
%NCDF_INC
......