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**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
==========
......
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/":$LD_LIBRARY_PATH
# mpi ifort compiler options for ZEUS cluster + XIOS
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
#
# CPP Pre-processor
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# FPPFLAGS pre-processing flags
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# AR assembler
# ARFLAGS assembler flags
# MK make (usually GNU make)
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." 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${XIOS}/lib -lxios
%USER_INC %XIOS_INC %NCDF_INC %HDF5_INC
%USER_LIB %XIOS_LIB %NCDF_LIB %HDF5_LIB
%FC mpiifort
%FCFLAGS -r8 -O3 -fp-model source -traceback -qmkl=cluster -march=icelake-client -mtune=icelake-client -qopt-zmm-usage=low -no-fma
%FFLAGS %FCFLAGS
%CC mpiicc
%CFLAGS -O0
%LD mpiifort
%LDFLAGS -lstdc++ -lgpfs
%AR ar
%ARFLAGS -r
%CPP icc
%FPPFLAGS -E -P -traditional
%MK gmake
arch-X64_JUNO.env
\ No newline at end of file
# mpi ifort compiler options for ZEUS cluster + XIOS
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
#
# CPP Pre-processor
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# FPPFLAGS pre-processing flags
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# AR assembler
# ARFLAGS assembler flags
# MK make (usually GNU make)
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." 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${XIOS}/lib -lxios
%USER_INC %XIOS_INC %NCDF_INC %HDF5_INC
%USER_LIB %XIOS_LIB %NCDF_LIB %HDF5_LIB
%FC mpiifort
%FCFLAGS -r8 -g -O0 -check all -fp-model source -traceback -qmkl=cluster -march=icelake-client -mtune=icelake-client -qopt-zmm-usage=low -no-fma
%FFLAGS %FCFLAGS
%CC mpiicc
%CFLAGS -O0
%LD mpiifort
%LDFLAGS -lstdc++ -lgpfs
%AR ar
%ARFLAGS -r
%CPP icc
%FPPFLAGS -E -P -traditional
%MK gmake
......@@ -54,5 +54,5 @@
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC cc
%CC icc
%CFLAGS -O0
......@@ -54,5 +54,5 @@
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC cc
%CC icc
%CFLAGS -O0
# compiler options for AA (using GCC compiler)
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
#
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# FPPFLAGS pre-processing flags
# AR assembler
# ARFLAGS assembler flags
# MK make
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." 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=${XIOS_DIR}/lib
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK make
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC gcc
%CFLAGS -O0 -fcommon
# compiler options for AA (using GCC compiler)
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
#
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# FPPFLAGS pre-processing flags
# AR assembler
# ARFLAGS assembler flags
# MK make
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." 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=${XIOS_DIR}/lib
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK make
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC gcc
%CFLAGS -O0 -fcommon
# compiler options for AA (using INTEL compiler & OpenMPI)
#
# module purge
# module use /home/ar0s/modules
# module load prgenv/intel intel/2021.4.0 openmpi/4.1.1.1 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/rev2320-nmpi
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
#
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# FPPFLAGS pre-processing flags
# AR assembler
# ARFLAGS assembler flags
# MK make
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." 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${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp
%FC mpifort -c -cpp
%FCFLAGS -march=core-avx2 -i4 -r8 -O3 -fp-model strict -fno-alias -align array64byte
%FFLAGS %FCFLAGS
%LD mpifort
%LDFLAGS
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK gmake
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC mpicc
%CFLAGS -O0
# compiler options for AA (using INTEL compiler & OpenMPI)
#
# module purge
# module use /home/ar0s/modules
# module load prgenv/intel intel/2021.4.0 openmpi/4.1.1.1 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/rev2320-nmpi
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
#
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# FPPFLAGS pre-processing flags
# AR assembler
# ARFLAGS assembler flags
# MK make
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." 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${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp
%FC mpifort -c -cpp
%FCFLAGS -march=core-avx2 -i4 -r8 -g -O0 -debug all -traceback -fp-model strict -ftrapuv -check all,noarg_temp_created -fpe-all0 -ftz -init=arrays,snan,huge
%FFLAGS %FCFLAGS
%LD mpifort
%LDFLAGS
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK gmake
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC mpicc
%CFLAGS -O0
# compiler options for BELENOS/TARANIS (using INTEL compiler)
# compiler options for BELENOS/TARANIS (using INTEL compiler + INTEL MPI)
#
# INTEL_IMPI (XIOS-2.5)
# intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios-2.5_rev1903
# --------------------------------
# INTEL_IMPI (NEMO 4.0 + XIOS-2.5)
# --------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/2.5/rev1903
#
# INTEL_IMPI (XIOS-TRUNK must be compiled)
# gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2
# ----------------------------------
# INTEL_IMPI (NEMO 4.2 + XIOS-TRUNK)
# ----------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/rev2134
#
#
# NCDF_INC netcdf4 include file
......@@ -44,7 +50,7 @@
%NCDF_LIB -L${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${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp
......
# compiler options for BELENOS/TARANIS (using INTEL compiler)
# compiler options for BELENOS/TARANIS (using INTEL compiler + INTEL MPI)
#
# INTEL_IMPI (XIOS-2.5)
# intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios-2.5_rev1903
# --------------------------------
# INTEL_IMPI (NEMO 4.0 + XIOS-2.5)
# --------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/2.5/rev1903
#
# INTEL_IMPI (XIOS-TRUNK must be compiled)
# gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2
# ----------------------------------
# INTEL_IMPI (NEMO 4.2 + XIOS-TRUNK)
# ----------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/rev2134
#
#
# NCDF_INC netcdf4 include file
......@@ -44,7 +50,7 @@
%NCDF_LIB -L${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
......
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<!--
==============================================================================================
NEMO context
==============================================================================================
-->
<context id="nemo">
<!-- $id$ -->
<!-- Fields definition -->
<field_definition src="./field_def_nemo-oce.xml"/> <!-- NEMO ocean dynamics -->
<field_definition src="./field_def_nemo-ice.xml"/> <!-- NEMO ocean sea ice -->
<!-- <field_definition src="./field_def_nemo-bgc.xml"/> --> <!-- NEMO ocean biogeochemistry with PISCES -->
<!-- Files definition -->
<file_definition src="./file_def_nemo-oce-BASIC.xml"/> <!-- NEMO ocean dynamics -->
<file_definition src="./file_def_nemo-ice-BASIC.xml"/> <!-- NEMO ocean sea ice -->
<!-- <file_definition src="./file_def_nemo-bgc.xml"/> --> <!-- NEMO ocean biogeochemistry with PISCES -->
<!--
============================================================================================================
= grid definition = = DO NOT CHANGE =
============================================================================================================
-->
<axis_definition>
<axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" />
<axis id="deptht300" axis_ref="deptht" >
<zoom_axis begin="0" n="35" />
</axis>
<axis id="depthu" long_name="Vertical U levels" unit="m" positive="down" />
<axis id="depthv" long_name="Vertical V levels" unit="m" positive="down" />
<axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
<axis id="nfloat" long_name="Float number" unit="-" />
<axis id="icbcla" long_name="Iceberg class" unit="1" />
<axis id="ncatice" long_name="Ice category" unit="1" />
<axis id="iax_20C" long_name="20 degC isotherm" unit="degC" />
<axis id="iax_28C" long_name="28 degC isotherm" unit="degC" />
<axis id="deptht_surface" axis_ref="deptht" >
<zoom_axis begin=" 0 " n=" 1 " />
</axis>
</axis_definition>
<domain_definition src="./domain_def_nemo.xml"/>
<grid_definition src="./grid_def_nemo.xml"/>
</context>
<!--
==============================================================================================
NEMO context
==============================================================================================
-->
<context id="nemo">
<!-- $id$ -->
<!-- Fields definition -->
<field_definition src="./field_def_nemo-oce.xml"/> <!-- NEMO ocean dynamics -->
<field_definition src="./field_def_nemo-ice.xml"/> <!-- NEMO ocean sea ice -->
<!-- <field_definition src="./field_def_nemo-bgc.xml"/> <!-- NEMO ocean biogeochemistry with PISCES -->
<!-- Files definition -->
<file_definition src="./file_def_nemo-oce-CMIP6.xml"/> <!-- NEMO ocean dynamics -->
<file_definition src="./file_def_nemo-ice-CMIP6.xml"/> <!-- NEMO ocean sea ice -->
<!-- <file_definition src="./file_def_nemo-bgc.xml"/> <!-- NEMO ocean biogeochemistry with PISCES -->
<!--
============================================================================================================
= grid definition = = DO NOT CHANGE =
============================================================================================================
-->
<axis_definition>
<axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" />
<axis id="deptht300" axis_ref="deptht" >
<zoom_axis begin="0" n="35" />
</axis>
<axis id="depthu" long_name="Vertical U levels" unit="m" positive="down" />
<axis id="depthv" long_name="Vertical V levels" unit="m" positive="down" />
<axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
<axis id="nfloat" long_name="Float number" unit="-" />
<axis id="icbcla" long_name="Iceberg class" unit="1" />
<axis id="ncatice" long_name="Ice category" unit="1" />
<axis id="iax_20C" long_name="20 degC isotherm" unit="degC" />
<axis id="iax_28C" long_name="28 degC isotherm" unit="degC" />
<axis id="deptht_surface" axis_ref="deptht" >
<zoom_axis begin=" 0 " n=" 1 " />
</axis>
</axis_definition>
<domain_definition src="./domain_def_nemo.xml"/>
<grid_definition src="./grid_def_nemo.xml"/>
</context>
......@@ -6,12 +6,15 @@
<context id="nemo">
<!-- $id$ -->
<!-- Fields definition -->
<field_definition src="./field_def_nemo-oce.xml"/> <!-- NEMO ocean dynamics -->
<field_definition src="./field_def_nemo-ice.xml"/> <!-- NEMO sea-ice model -->
<field_definition src="./field_def_nemo-oce.xml"/> <!-- NEMO ocean dynamics -->
<field_definition src="./field_def_nemo-ice.xml"/> <!-- NEMO ocean sea ice -->
<!-- <field_definition src="./field_def_nemo-bgc.xml"/> <!-- NEMO ocean biogeochemistry with PISCES -->
<!-- Files definition -->
<file_definition src="./file_def_nemo-oce.xml"/> <!-- NEMO ocean dynamics -->
<file_definition src="./file_def_nemo-ice.xml"/> <!-- NEMO sea-ice model -->
<file_definition src="./file_def_nemo-oce.xml"/> <!-- NEMO ocean dynamics -->
<file_definition src="./file_def_nemo-ice.xml"/> <!-- NEMO ocean sea ice -->
<!-- <file_definition src="./file_def_nemo-bgc.xml"/> <!-- NEMO ocean biogeochemistry with PISCES -->
<!--
============================================================================================================
= grid definition = = DO NOT CHANGE =
......@@ -20,22 +23,24 @@
<axis_definition>
<axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" />
<axis id="deptht300" axis_ref="deptht" >
<zoom_axis begin="0" n="35" />
</axis>
<axis id="depthu" long_name="Vertical U levels" unit="m" positive="down" />
<axis id="depthv" long_name="Vertical V levels" unit="m" positive="down" />
<axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
<axis id="profsed" long_name="Vertical S levels" unit="cm" positive="down" />
<axis id="nfloat" long_name="Float number" unit="-" />
<axis id="icbcla" long_name="Iceberg class" unit="1" />
<axis id="ncatice" long_name="Ice category" unit="1" />
<axis id="iax_20C" long_name="20 degC isotherm" unit="degC" />
<axis id="iax_28C" long_name="28 degC isotherm" unit="degC" />
<!-- ABL vertical axis definition -->
<axis id="ght_abl" long_name="ABL Vertical T levels" unit="m" positive="up" />
<axis id="ghw_abl" long_name="ABL Vertical W levels" unit="m" positive="up" />
<axis id="deptht_surface" axis_ref="deptht" >
<zoom_axis begin=" 0 " n=" 1 " />
</axis>
</axis_definition>
<domain_definition src="./domain_def_nemo.xml"/>
<grid_definition src="./grid_def_nemo.xml"/>
</context>
<?xml version="1.0"?>
<!-- $id$ -->
<!--
============================================================================================================
= output files definition =
= Define your own files for sea ice =
= put the variables you want... =
============================================================================================================
-->
<file_definition type="one_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4">
<file_group id="10d" output_freq="10d" output_level="10" enabled=".TRUE."> <!-- 10d files -->
<file id="file21" name_suffix="_icemod" description="ice variables" enabled=".true." >
<!-- ice mask -->
<field field_ref="icemask" name="simsk" />
<field field_ref="icemask05" name="simsk05" />
<field field_ref="icemask15" name="simsk15" />
<!-- general -->
<field field_ref="snwvolu" name="snvolu" />
<field field_ref="icethic" name="sithic" />
<field field_ref="icevolu" name="sivolu" />
<field field_ref="iceconc" name="siconc" />
<field field_ref="icesalt" name="sisali" />
<field field_ref="iceapnd" name="siapnd" />
<field field_ref="icevpnd" name="sivpnd" />
<field field_ref="iceepnd" name="siepnd" />
<field field_ref="icevlid" name="sivlid" />
<!-- sst_m is always the potential temperature even when using teos10 -->
<field field_ref="sst_m_pot" name="sst_m_pot" />
<field field_ref="sss_m_abs" name="sss_m_abs" />
<!-- heat -->
<field field_ref="icetemp" name="sitemp" />
<field field_ref="icettop" name="sittop" />
<field field_ref="icetbot" name="sitbot" />
<field field_ref="icetsni" name="sitsni" />
<!-- ponds -->
<field field_ref="dvpn_mlt" name="dvpn_mlt" />
<field field_ref="dvpn_lid" name="dvpn_lid" />
<field field_ref="dvpn_rnf" name="dvpn_rnf" />
<field field_ref="dvpn_drn" name="dvpn_drn" />
<!-- momentum -->
<field field_ref="uice" name="sivelu" />
<field field_ref="vice" name="sivelv" />
<field field_ref="icevel" name="sivelo" />
<field field_ref="utau_ai" name="utau_ai" />
<field field_ref="vtau_ai" name="vtau_ai" />
<field field_ref="utau_oi" name="utau_oi" />
<field field_ref="vtau_oi" name="vtau_oi" />
<!-- rheology -->
<field field_ref="icediv" name="sidive" />
<field field_ref="iceshe" name="sishea" />
<field field_ref="icestr" name="sistre" />
<field field_ref="normstr" name="normstr" />
<field field_ref="sheastr" name="sheastr" />
<field field_ref="isig1" name="isig1" />
<field field_ref="isig2" name="isig2" />
<field field_ref="isig3" name="isig3" />
<!-- heat fluxes -->
<field field_ref="qt_oce_ai" name="qt_oce_ai" />
<field field_ref="qt_atm_oi" name="qt_atm_oi" />
<field field_ref="qtr_ice_top" name="qtr_ice_top"/>
<field field_ref="qtr_ice_bot" name="qtr_ice_bot"/>
<field field_ref="qt_ice" name="qt_ice" />
<field field_ref="qsr_ice" name="qsr_ice" />
<field field_ref="qns_ice" name="qns_ice" />
<field field_ref="qemp_ice" name="qemp_ice" />
<field field_ref="albedo" name="albedo" />
<field field_ref="hfxcndtop" name="hfxcndtop" />
<field field_ref="hfxcndbot" name="hfxcndbot" />
<field field_ref="hfxsensib" name="hfxsensib" />
<!-- salt fluxes -->
<field field_ref="sfxice" name="sfxice" />
<!-- mass fluxes -->
<field field_ref="vfxice" name="vfxice" />
<field field_ref="vfxsnw" name="vfxsnw" />
<!-- categories -->
<field field_ref="icemask_cat" name="simskcat"/>
<field field_ref="snwthic_cat" name="snthicat"/>
<field field_ref="iceconc_cat" name="siconcat"/>
<field field_ref="icethic_cat" name="sithicat"/>
<field field_ref="icesalt_cat" name="sisalcat"/>
<field field_ref="icetemp_cat" name="sitemcat"/>
<field field_ref="iceapnd_cat" name="siapncat"/>
<field field_ref="icevpnd_cat" name="sivpncat"/>
<field field_ref="snwtemp_cat" name="sntemcat"/>
<!-- mass balance -->
<field field_ref="dmithd" name="sidmassth" />
<field field_ref="dmidyn" name="sidmassdyn" />
<field field_ref="dmiopw" name="sidmassgrowthwat" />
<field field_ref="dmibog" name="sidmassgrowthbot" />
<field field_ref="dmisni" name="sidmasssi" />
<field field_ref="dmisub" name="sidmassevapsubl" />
<field field_ref="dmisum" name="sidmassmelttop" />
<field field_ref="dmibom" name="sidmassmeltbot" />
<field field_ref="dmilam" name="sidmassmeltlat" />
<field field_ref="dmsspr" name="sndmasssnf" />
<field field_ref="dmsmel" name="sndmassmelt" />
<field field_ref="dmssub" name="sndmasssubl" />
<field field_ref="dmsdyn" name="sndmassdyn" />
<field field_ref="dmsssi" name="sndmasssi" />
</file>
<file id="file22" name_suffix="_SBC_scalar" description="scalar variables" enabled=".true." >
<!-- global contents -->
<field field_ref="ibgvol_tot" name="ibgvol_tot" />
<field field_ref="sbgvol_tot" name="sbgvol_tot" />
<field field_ref="ibgarea_tot" name="ibgarea_tot" />
<field field_ref="ibgsalt_tot" name="ibgsalt_tot" />
<field field_ref="ibgheat_tot" name="ibgheat_tot" />
<field field_ref="sbgheat_tot" name="sbgheat_tot" />
<!-- global drifts (conservation checks) -->
<field field_ref="ibgvolume" name="ibgvolume" />
<field field_ref="ibgsaltco" name="ibgsaltco" />
<field field_ref="ibgheatco" name="ibgheatco" />
<field field_ref="ibgheatfx" name="ibgheatfx" />
<!-- global forcings -->
<field field_ref="ibgfrcvoltop" name="ibgfrcvoltop" />
<field field_ref="ibgfrcvolbot" name="ibgfrcvolbot" />
<field field_ref="ibgfrctemtop" name="ibgfrctemtop" />
<field field_ref="ibgfrctembot" name="ibgfrctembot" />
<field field_ref="ibgfrcsal" name="ibgfrcsal" />
<field field_ref="ibgfrchfxtop" name="ibgfrchfxtop" />
<field field_ref="ibgfrchfxbot" name="ibgfrchfxbot" />
</file>
</file_group>
<file_group id="1ts" output_freq="1ts" output_level="10" enabled=".TRUE."/> <!-- 1 time step files -->
<file_group id="1h" output_freq="1h" output_level="10" enabled=".TRUE."/> <!-- 1h files -->
<file_group id="2h" output_freq="2h" output_level="10" enabled=".TRUE."/> <!-- 2h files -->
<file_group id="3h" output_freq="3h" output_level="10" enabled=".TRUE."/> <!-- 3h files -->
<file_group id="4h" output_freq="4h" output_level="10" enabled=".TRUE."/> <!-- 4h files -->
<file_group id="6h" output_freq="6h" output_level="10" enabled=".TRUE."/> <!-- 6h files -->
<file_group id="1m" output_freq="1mo" output_level="10" enabled=".TRUE."/> <!-- real monthly files -->
<file_group id="2m" output_freq="2mo" output_level="10" enabled=".TRUE."/> <!-- real 2m files -->
<file_group id="3m" output_freq="3mo" output_level="10" enabled=".TRUE."/> <!-- real 3m files -->
<file_group id="4m" output_freq="4mo" output_level="10" enabled=".TRUE."/> <!-- real 4m files -->
<file_group id="6m" output_freq="6mo" output_level="10" enabled=".TRUE."/> <!-- real 6m files -->
<file_group id="1y" output_freq="1y" output_level="10" enabled=".TRUE."/> <!-- real yearly files -->
<file_group id="2y" output_freq="2y" output_level="10" enabled=".TRUE."/> <!-- real 2y files -->
<file_group id="5y" output_freq="5y" output_level="10" enabled=".TRUE."/> <!-- real 5y files -->
<file_group id="10y" output_freq="10y" output_level="10" enabled=".TRUE."/> <!-- real 10y files -->
</file_definition>
......@@ -11,7 +11,7 @@
<file_definition type="one_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4">
<file_group id="5d" output_freq="5d" output_level="10" enabled=".TRUE."> <!-- 5d files -->
<file_group id="1m" output_freq="1mo" output_level="10" enabled=".TRUE."> <!-- 1m files -->
<file id="file21" name_suffix="_icemod" description="ice variables" enabled=".true." >
<!-- ice mask -->
......@@ -27,15 +27,23 @@
<field field_ref="icesalt" name="sisali" />
<field field_ref="iceapnd" name="siapnd" />
<field field_ref="icevpnd" name="sivpnd" />
<field field_ref="sst_m" name="sst_m" />
<field field_ref="sss_m" name="sss_m" />
<field field_ref="iceepnd" name="siepnd" />
<field field_ref="icevlid" name="sivlid" />
<!-- sst_m is always the potential temperature even when using teos10 -->
<field field_ref="sst_m_pot" name="sst_m_pot" />
<field field_ref="sss_m_abs" name="sss_m_abs" />
<!-- heat -->
<field field_ref="icetemp" name="sitemp" />
<field field_ref="snwtemp" name="sntemp" />
<field field_ref="icettop" name="sittop" />
<field field_ref="icetbot" name="sitbot" />
<field field_ref="icetsni" name="sitsni" />
<!-- ponds -->
<field field_ref="dvpn_mlt" name="dvpn_mlt" />
<field field_ref="dvpn_lid" name="dvpn_lid" />
<field field_ref="dvpn_rnf" name="dvpn_rnf" />
<field field_ref="dvpn_drn" name="dvpn_drn" />
<!-- momentum -->
<field field_ref="uice" name="sivelu" />
......@@ -52,8 +60,8 @@
<field field_ref="icestr" name="sistre" />
<field field_ref="normstr" name="normstr" />
<field field_ref="sheastr" name="sheastr" />
<field field_ref="sig1_pnorm" name="sig1_pnorm"/>
<field field_ref="sig2_pnorm" name="sig2_pnorm"/>
<field field_ref="sig1_pnorm" name="isig1" />
<field field_ref="sig2_pnorm" name="isig2" />
<!-- heat fluxes -->
<field field_ref="qt_oce_ai" name="qt_oce_ai" />
......@@ -84,34 +92,51 @@
<field field_ref="icethic_cat" name="sithicat"/>
<field field_ref="icesalt_cat" name="sisalcat"/>
<field field_ref="icetemp_cat" name="sitemcat"/>
<field field_ref="iceapnd_cat" name="siapncat"/>
<field field_ref="icevpnd_cat" name="sivpncat"/>
<field field_ref="snwtemp_cat" name="sntemcat"/>
<field field_ref="icettop_cat" name="sitopcat"/>
<!-- mass balance -->
<field field_ref="dmithd" name="sidmassth" />
<field field_ref="dmidyn" name="sidmassdyn" />
<field field_ref="dmiopw" name="sidmassgrowthwat" />
<field field_ref="dmibog" name="sidmassgrowthbot" />
<field field_ref="dmisni" name="sidmasssi" />
<field field_ref="dmisub" name="sidmassevapsubl" />
<field field_ref="dmisum" name="sidmassmelttop" />
<field field_ref="dmibom" name="sidmassmeltbot" />
<field field_ref="dmilam" name="sidmassmeltlat" />
<field field_ref="dmsspr" name="sndmasssnf" />
<field field_ref="dmsmel" name="sndmassmelt" />
<field field_ref="dmssub" name="sndmasssubl" />
<field field_ref="dmsdyn" name="sndmassdyn" />
<field field_ref="dmsssi" name="sndmasssi" />
</file>
<file id="file22" name_suffix="_SBC_scalar" description="scalar variables" enabled=".true." >
<!-- global contents -->
<field field_ref="ibgvol_tot" name="ibgvol_tot" />
<field field_ref="sbgvol_tot" name="sbgvol_tot" />
<field field_ref="ibgarea_tot" name="ibgarea_tot" />
<field field_ref="ibgsalt_tot" name="ibgsalt_tot" />
<field field_ref="ibgheat_tot" name="ibgheat_tot" />
<field field_ref="sbgheat_tot" name="sbgheat_tot" />
<field field_ref="ibgvol_tot" name="ibgvol_tot" />
<field field_ref="sbgvol_tot" name="sbgvol_tot" />
<field field_ref="ibgarea_tot" name="ibgarea_tot" />
<field field_ref="ibgsalt_tot" name="ibgsalt_tot" />
<field field_ref="ibgheat_tot" name="ibgheat_tot" />
<field field_ref="sbgheat_tot" name="sbgheat_tot" />
<!-- global drifts (conservation checks) -->
<field field_ref="ibgvolume" name="ibgvolume" />
<field field_ref="ibgsaltco" name="ibgsaltco" />
<field field_ref="ibgheatco" name="ibgheatco" />
<field field_ref="ibgheatfx" name="ibgheatfx" />
<field field_ref="ibgvolume" name="ibgvolume" />
<field field_ref="ibgsaltco" name="ibgsaltco" />
<field field_ref="ibgheatco" name="ibgheatco" />
<field field_ref="ibgheatfx" name="ibgheatfx" />
<!-- global forcings -->
<field field_ref="ibgfrcvoltop" name="ibgfrcvoltop" />
<field field_ref="ibgfrcvolbot" name="ibgfrcvolbot" />
<field field_ref="ibgfrctemtop" name="ibgfrctemtop" />
<field field_ref="ibgfrctembot" name="ibgfrctembot" />
<field field_ref="ibgfrcsal" name="ibgfrcsal" />
<field field_ref="ibgfrchfxtop" name="ibgfrchfxtop" />
<field field_ref="ibgfrchfxbot" name="ibgfrchfxbot" />
<field field_ref="ibgfrcvoltop" name="ibgfrcvoltop" />
<field field_ref="ibgfrcvolbot" name="ibgfrcvolbot" />
<field field_ref="ibgfrctemtop" name="ibgfrctemtop" />
<field field_ref="ibgfrctembot" name="ibgfrctembot" />
<field field_ref="ibgfrcsal" name="ibgfrcsal" />
<field field_ref="ibgfrchfxtop" name="ibgfrchfxtop" />
<field field_ref="ibgfrchfxbot" name="ibgfrchfxbot" />
</file>
</file_group>
......
You can't use the standard diagnostic options with the current cycling period.
Choose the "Custom" option, copy the file_def*.xml files that
you want to use into the Rose app and adjust the meaning period
accordingly.