.gitlab/issue_templates/Bug.md

+#### 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

+#### 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

+#### 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

+

.gitlab/merge_request_templates/Task_review.md

+#### 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?

README.rst

-**Contents**
+NEMO
+====
 
-.. contents::
-   :local:
-
-
-
-
-.. _`Former web platform forge`: https://forge.ipsl.jussieu.fr/nemo
-.. _`NEMO users' guide`: https://sites.nemo-ocean.io/user-guide
-.. _`Migration Guide`: https://sites.nemo-ocean.io/user-guide/migration.html
-.. _`Change list`: https://sites.nemo-ocean.io/user-guide/changes.html
-.. _`Test case repository`: https://github.com/NEMO-ocean/NEMO-examples
-.. _`How to cite`: https://www.nemo-ocean.eu/bibliography/how-to-cite/
-.. _`NEMO forums`: https://nemo-ocean.discourse.group
-.. _`NEMO newsletter`: https://listes.ipsl.fr/sympa/subscribe/nemo-newsletter
-.. _`NEMO publications`: https://www.nemo-ocean.eu/bibliography/publications/add
-.. _`NEMO projects`: https://www.nemo-ocean.eu/projects/add
-.. _`Special Issue`: https://gmd.copernicus.org/articles/special_issue40.html
-.. _`NEMO System Team wiki`: https://forge.nemo-ocean.eu/developers/home/-/wikis/Home
-.. _`NEMO ocean engine`: https://zenodo.org/record/1464816
-.. _`NEMO Tracers engine` : https://zenodo.org/record/1471700
-.. _`NEMO Sea Ice engine`: https://zenodo.org/record/1471689
-
-
-**Welcome to NEMO home page!**
-  
-NEMO (*Nucleus for European Modelling of the Ocean*) is a state-of-the-art modelling
+*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 you to get started using the NEMO platform and to introduce you
-to the different levels of information available. It starts here with NEMO release 4.2.0.
-
-Reminder: Our `Former web platform forge`_ (SVN+Trac) contains the previous documentation
-and releases made available from the beginning of the project up to of NEMO 4.0.
-
-Getting started
-===============
-
-Getting your hands on NEMO: the first steps are described in detail in the 
-`NEMO users' guide`_ . This explains how to download the code, build the environment, 
-create the executable, and perform a first integration.
-
-If you are already using a previous release of NEMO, please refer to the 
-`Migration Guide`_ which aims to help you to make 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, a set of test cases is also available from the
-`Test case repository`_ . These test cases can be useful for students, outreach, and
-exploring specific aspects of NEMO with light configurations. The web page also allows you
-to submit test cases you have developed and want to share with the community. Feel free to
-contribute!
-
-
-Project documentation
-=====================
-
-Reference manuals fully describing NEMO  for the three main component
-
-* |OCE| models the ocean {thermo}dynamics and solves the primitive equations (`./src/OCE <./src/OCE>`_)
-
-* |ICE| simulates sea-ice {thermo}dynamics, brine inclusions and subgrid-scale thickness 
-  variations (`./src/ICE <./src/ICE>`_)
-
-* |MBG| models the {on,off}line oceanic tracers transport and biogeochemical processes 
-  (`./src/TOP <./src/TOP>`_)
-are available from Zenodo:
-
-============ ======================== =====
- Component    Reference Manual         DOI
-============ ======================== =====
- |NEMO-OCE|   `NEMO ocean engine`_    .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6334656.svg
-                                         :target: https://doi.org/10.5281/zenodo.6334656                        
- |NEMO-ICE|   `NEMO Sea Ice engine`_  *not yet available*
- |NEMO-MBG|   `NEMO Tracers engine`_  .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg
-                                         :target: https://doi.org/10.5281/zenodo.1471700
-============ ======================== =====
-
-These reference manuals are the publications that should be cited in your own
-publications. Please visit `How to cite`_? for details.
-
-New features of 4.2.0 release are described in the `Change list`_ section of the `NEMO users' guide`_
-
-
-Asking questions, and exchanging information
-============================================
-- Register once for all and use the `NEMO forums`_ on discourse to share and discuss with the NEMO community.
-
-- Register once for all and receive by mail the `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 to the `NEMO publications`_ page
-
--  Describing your project using NEMO on the `NEMO projects`_ page
-
-NEMO also has a `Special Issue`_ in the open-access journal
-Geoscientific Model Development (GMD) from the European Geosciences Union
-The main scope is to collect relevant manuscripts covering various topics and
-to provide a single portal to assess the model potential and evolution.
-
-
-
-Contributing to NEMO development
-================================
+For all information please refer to the `NEMO wiki <https://forge.nemo-ocean.eu/nemo/nemo/-/wikis/home>`_
 
-NEMO strives to be written in a way which allows the easy incorporation of developments.
-You are 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 is
-available on the `NEMO System Team wiki`_
+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
 ==========

arch/CMCC/arch-X64_JUNO.env

+
+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

+# 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

+arch-X64_JUNO.env
\ No newline at end of file

arch/CMCC/arch-X64_JUNO_DEBUG.fcm

+# 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/CNRS/arch-X64_IRENE.fcm

@@ -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

@@ -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/MERCATOR/arch-X64_AA_GCC_OMPI.fcm

+# compiler options for AA (using GCC compiler)
+#
+#
+# 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)
+# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
+# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
+#
+# FC          Fortran compiler command
+# FCFLAGS     Fortran compiler flags
+# FFLAGS      Fortran 77 compiler flags
+# LD          linker
+# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
+# FPPFLAGS    pre-processing flags
+# AR          assembler
+# ARFLAGS     assembler flags
+# MK          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 $)
+#
+#---------------------------------------------------------------------------------------------
+#---------------------------------------------------------------------------------------------
+# All NETCDF and HDF paths are empty as they are automatically defined through environment
+# variables by the load of modules
+#---------------------------------------------------------------------------------------------
+#---------------------------------------------------------------------------------------------
+#
+#
+%NCDF_INC            ${NETCDF4_INCLUDE}
+%NCDF_LIB            -L${NETCDF4_DIR}/lib -lnetcdff -lnetcdf -L${HDF5_DIR}/lib -lhdf5_hl -lm
+%XIOS_INC            -I${XIOS_INC}
+%XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
+%OASIS_INC           -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
+%OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
+
+%CPP                 cpp -Dkey_nosignedzero
+%FC                  mpif90 -c -cpp
+# O3 breaks reproduci/restartabi-lity with gcc/12.2.0
+%FCFLAGS             -fdefault-real-8 -O2 -funroll-all-loops -fcray-pointer -ffree-line-length-none -fallow-argument-mismatch -Wno-missing-include-dirs
+%FFLAGS              %FCFLAGS
+%LD                  mpif90
+%LDFLAGS             -Wl,-rpath,${HDF5_DIR}/lib -Wl,-rpath=${NETCDF4_DIR}/lib -Wl,-rpath=${XIOS_DIR}/lib
+%FPPFLAGS            -P -traditional
+%AR                  ar
+%ARFLAGS             rs
+%MK                  make
+%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
+
+%CC                  gcc
+%CFLAGS              -O0 -fcommon

arch/MERCATOR/arch-X64_AA_GCC_OMPI_DEBUG.fcm

+# compiler options for AA (using GCC compiler)
+#
+#
+# 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)
+# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
+# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
+#
+# FC          Fortran compiler command
+# FCFLAGS     Fortran compiler flags
+# FFLAGS      Fortran 77 compiler flags
+# LD          linker
+# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
+# FPPFLAGS    pre-processing flags
+# AR          assembler
+# ARFLAGS     assembler flags
+# MK          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 $)
+#
+#---------------------------------------------------------------------------------------------
+#---------------------------------------------------------------------------------------------
+# All NETCDF and HDF paths are empty as they are automatically defined through environment
+# variables by the load of modules
+#---------------------------------------------------------------------------------------------
+#---------------------------------------------------------------------------------------------
+#
+#
+%NCDF_INC            ${NETCDF4_INCLUDE}
+%NCDF_LIB            -L${NETCDF4_DIR}/lib -lnetcdff -lnetcdf -L${HDF5_DIR}/lib -lhdf5_hl -lm
+%XIOS_INC            -I${XIOS_INC}
+%XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
+%OASIS_INC           -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
+%OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
+
+%CPP                 cpp -Dkey_nosignedzero
+%FC                  mpif90 -c -cpp
+%FCFLAGS       -fdefault-real-8 -Og -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all,no-array-temps -finit-real=nan -ffpe-trap=invalid,zero,overflow -ffpe-summary=invalid,zero,overflow -fallow-argument-mismatch -Wno-missing-include-dirs
+%FFLAGS              %FCFLAGS
+%LD                  mpif90
+%LDFLAGS             -Wl,-rpath,${HDF5_DIR}/lib -Wl,-rpath=${NETCDF4_DIR}/lib -Wl,-rpath=${XIOS_DIR}/lib
+%FPPFLAGS            -P -traditional
+%AR                  ar
+%ARFLAGS             rs
+%MK                  make
+%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
+
+%CC                  gcc
+%CFLAGS              -O0 -fcommon

arch/MERCATOR/arch-X64_AA_INTEL_OMPI.fcm

+# compiler options for AA (using INTEL compiler & OpenMPI)
+#
+# module purge
+# module use /home/ar0s/modules
+# module load prgenv/intel intel/2021.4.0 openmpi/4.1.1.1 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/rev2320-nmpi
+#
+#
+# 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)
+# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
+# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
+#
+# FC          Fortran compiler command
+# FCFLAGS     Fortran compiler flags
+# FFLAGS      Fortran 77 compiler flags
+# LD          linker
+# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
+# FPPFLAGS    pre-processing flags
+# AR          assembler
+# ARFLAGS     assembler flags
+# MK          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 $)
+#
+#---------------------------------------------------------------------------------------------
+#---------------------------------------------------------------------------------------------
+# All NETCDF and HDF paths are empty as they are automatically defined through environment
+# variables by the load of modules
+#---------------------------------------------------------------------------------------------
+#---------------------------------------------------------------------------------------------
+#
+#
+%NCDF_INC            ${NETCDF4_INCLUDE}
+%NCDF_LIB            ${NETCDF4_LIB} -L${HDF5_DIR}/lib -Wl,-rpath,${HDF5_DIR}/lib -lhdf5_hl -lhdf5 -lz
+%XIOS_INC            -I${XIOS_INC}
+%XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
+%OASIS_INC           -I${OASIS_DIR}/include
+%OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
+
+%CPP                 cpp
+%FC                  mpifort -c -cpp
+%FCFLAGS             -march=core-avx2 -i4 -r8 -O3 -fp-model strict -fno-alias -align array64byte
+%FFLAGS              %FCFLAGS
+%LD                  mpifort
+%LDFLAGS             
+%FPPFLAGS            -P -traditional
+%AR                  ar
+%ARFLAGS             rs
+%MK                  gmake
+%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
+
+%CC                  mpicc
+%CFLAGS              -O0

arch/MERCATOR/arch-X64_AA_INTEL_OMPI_DEBUG.fcm

+# compiler options for AA (using INTEL compiler & OpenMPI)
+#
+# module purge
+# module use /home/ar0s/modules
+# module load prgenv/intel intel/2021.4.0 openmpi/4.1.1.1 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/rev2320-nmpi
+#
+#
+# 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)
+# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
+# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
+#
+# FC          Fortran compiler command
+# FCFLAGS     Fortran compiler flags
+# FFLAGS      Fortran 77 compiler flags
+# LD          linker
+# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
+# FPPFLAGS    pre-processing flags
+# AR          assembler
+# ARFLAGS     assembler flags
+# MK          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 $)
+#
+#---------------------------------------------------------------------------------------------
+#---------------------------------------------------------------------------------------------
+# All NETCDF and HDF paths are empty as they are automatically defined through environment
+# variables by the load of modules
+#---------------------------------------------------------------------------------------------
+#---------------------------------------------------------------------------------------------
+#
+#
+%NCDF_INC            ${NETCDF4_INCLUDE}
+%NCDF_LIB            ${NETCDF4_LIB} -L${HDF5_DIR}/lib -Wl,-rpath,${HDF5_DIR}/lib -lhdf5_hl -lhdf5 -lz
+%XIOS_INC            -I${XIOS_INC}
+%XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
+%OASIS_INC           -I${OASIS_DIR}/include
+%OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
+
+%CPP                 cpp
+%FC                  mpifort -c -cpp
+%FCFLAGS             -march=core-avx2 -i4 -r8 -g -O0 -debug all -traceback -fp-model strict -ftrapuv -check all,noarg_temp_created -fpe-all0 -ftz -init=arrays,snan,huge
+%FFLAGS              %FCFLAGS
+%LD                  mpifort
+%LDFLAGS             
+%FPPFLAGS            -P -traditional
+%AR                  ar
+%ARFLAGS             rs
+%MK                  gmake
+%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
+
+%CC                  mpicc
+%CFLAGS              -O0

arch/MERCATOR/arch-X64_BELENOS_INTEL_IMPI.fcm

-# compiler options for BELENOS/TARANIS (using INTEL compiler)
+# compiler options for BELENOS/TARANIS (using INTEL compiler + INTEL MPI)
 #
-# INTEL_IMPI (XIOS-2.5)
-# intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios-2.5_rev1903
+# --------------------------------
+# INTEL_IMPI (NEMO 4.0 + XIOS-2.5)
+# --------------------------------
+# module use /home/ext/mr/smer/samsong/modules
+# module load intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/2.5/rev1903
 #
-# INTEL_IMPI (XIOS-TRUNK must be compiled)
-# gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2
+# ----------------------------------
+# INTEL_IMPI (NEMO 4.2 + XIOS-TRUNK)
+# ----------------------------------
+# module use /home/ext/mr/smer/samsong/modules
+# module load gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/rev2134
 #
 #
 # NCDF_INC    netcdf4 include file
@@ -44,7 +50,7 @@
 %NCDF_LIB            -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${PHDF5_LIB_DIR} -lhdf5_hl -lhdf5
 %XIOS_INC            -I${XIOS_INC}
 %XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
-%OASIS_INC           -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
+%OASIS_INC           -I${OASIS_DIR}/include
 %OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
 
 %CPP                 cpp

arch/MERCATOR/arch-X64_BELENOS_INTEL_IMPI_DEBUG.fcm

-# compiler options for BELENOS/TARANIS (using INTEL compiler)
+# compiler options for BELENOS/TARANIS (using INTEL compiler + INTEL MPI)
 #
-# INTEL_IMPI (XIOS-2.5)
-# intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios-2.5_rev1903
+# --------------------------------
+# INTEL_IMPI (NEMO 4.0 + XIOS-2.5)
+# --------------------------------
+# module use /home/ext/mr/smer/samsong/modules
+# module load intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/2.5/rev1903
 #
-# INTEL_IMPI (XIOS-TRUNK must be compiled)
-# gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2
+# ----------------------------------
+# INTEL_IMPI (NEMO 4.2 + XIOS-TRUNK)
+# ----------------------------------
+# module use /home/ext/mr/smer/samsong/modules
+# module load gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/rev2134
 #
 #
 # NCDF_INC    netcdf4 include file
@@ -44,7 +50,7 @@
 %NCDF_LIB            -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${PHDF5_LIB_DIR} -lhdf5_hl -lhdf5
 %XIOS_INC            -I${XIOS_INC}
 %XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
-%OASIS_INC           -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
+%OASIS_INC           -I${OASIS_DIR}/include
 %OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
 
 %CPP                 cpp

cfgs/GYRE_BFM/EXPREF/context_nemo.xml

@@ -19,12 +19,13 @@
     </variable_definition>
 
 <!-- Fields definition -->
-    <field_definition src="./field_def_nemo-oce.xml"/>      <!--  NEMO ocean dynamics                     -->
-    <field_definition src="./field_def_nemo-pisces.xml"/>   <!--  NEMO ocean dynamics                     -->
+    <field_definition src="./field_def_nemo-oce.xml"/>    <!--  NEMO ocean dynamics    -->
+    <field_definition src="./field_def_bfm.xml"/>         <!--  BFM BGC  dynamics      -->
 
 
 <!-- Files definition -->
-    <file_definition src="./file_def_nemo.xml"/>     <!--  NEMO ocean dynamics                     -->
+    <file_definition src="./file_def_nemo.xml"/>          <!--  NEMO ocean dynamics    -->
+    <file_definition src="./file_def_bfm.xml"/>           <!-- BFM BGC dynamics        -->
 
 <!-- Axis definition -->
     <axis_definition src="./axis_def_nemo.xml"/>