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Version v4.0 – NEMO

Version v4.0

Released 5 years ago (2019-01-29T20:01:01+01:00)

Release note
  • AGRIF for embedded zooms:
    • Now compatible with new sea ice component
    • Now compatible with z* coordinate
    • Extended ghost cells area to properly handle scheme with spatial order >2
    • Added vertical refinement (beta)
    • Nesting tools for setup now up to date and working
  • Enhancements
    • Fix for tracer conservation with split explicit free surface
    • Bulk formulae : move to aerobulk package (Brodeau et al. 2016), i.e. NCAR, COARE and ECMWF bulk (remove Clio and MFS bulk)
    • Wetting and drying
    • Added tidal self attraction and loading either read from a file or from usual "scalar" approximation
    • Add a 4th order centered (CEN) and Flux Corrected Transport (FCT) tracer advection (using a 4th compact in the vertical)
    • iso-neutral mixing (iso and triad operators): add the Method of Stabilizing Correction (MSC) (more accurate calculation) + add a bilaplacian case
    • Lateral physics (LDF): scale aware setting of eddy viscosity and diffusivity
    • Vorticity: 2 new energy conserving scheme: ENT with Coriolis defined at T-point (better for Flux form) and EET a variant of EEN where e3t is used instead of e3f (solved the issue with e3f specification but is not enstrophy conserving)
  • Test Cases The first test cases available for now are:
    • CANAL: east-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex)
    • ICEDYN: east-west + north-south periodic channel. The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys.
    • ISOMIP: simple box configuration with an ice shelf with simple geometry on top. The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. The exact original setup is described here.
    • LOCK-EXCHANGE:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing
    • OVERFLOW: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012)
    • VORTEX: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991)
    • WAD: a set of simple closed basin geometries for testing the Wetting and drying capabilities. Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge.
  • New Reference configurations
    • AGRIF_DEMO: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator
    • SPITZ12: regional configuration around the Svalbard archipelago
  • Wave coupling
    • Coupled interface to external wave model
    • Large scale wave interaction process added in momentum and tracer equations
  • New sea-ice component SI3 (in place of LIMx)
    • Improvements in physics
      • Landfast ice: simple grounding with a "release" stress (not fully operational)
      • Lateral melting
      • Melt ponds: constant or Holland 2012 formulation (and soon topographic melt ponds)
      • Ice-atm. drags from Lupkes 2012 (depending on ice concentration) or Lupkes 2015 (depending on sea ice concentration and atm. stability)
    • Improvements in numerics
      • Advection: Ultimate-Macho scheme
      • Rheology: adaptive EVP (Kimmritz 2017)
      • Coupling interface: conductivity as surface forcing instead of heat fluxes (Met-Office requirement)
    • Improvements in performance
      • All thermodynamics in 1D
      • Reduced mpp communications
    • Users & developers friendly
      • Comprehensive set of outputs (universal units and understandable names + includes cmip)
      • New architecture and namelist
      • All processes can be decoupled from each other (switch on/off)
      • Ice categories bounds can be defined by the user or set automatically
      • For open boundaries, the number of ice categories from the forcing model can be different from the number of categories in the regional simulation
      • Fully compatible with AGRIF
  • Passive tracer TOP and biogeochemical PISCES components
    • The passive tracers transport component was redesigned toward a modular structure and users can enable each module directly through logical flags in namelist_top (no more fortran macros!).
    • TOP on-line user documentation is available on NEMO Trac platform (TOP-UserQuickGuide)
    • TOP currently accounts for the following 5 modules: CFC contains inorganic carbon tracers (CFC11/CFC12/SF6), MY_TRC is a template for new modules (or external couplings), AGE deals with water age tracking, C14 as a radiocarbon passive tracer, and the companion ecosystem model PISCES.
    • A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer.
    • A new configuration, named ORCA2_OFF_TRC, was created to provide a benchmark simulation environment to deal with inert carbon tracers dynamics by exploiting the offline coupling with NEMO.
    • PISCES model contains new developments and modifications:
      • Particulate Organic Carbon (POC) component comes with a new liability scheme, while the former Kriest parametrisation was superseded;
      • A complex iron chemistry scheme is now available, with an improved description of ligands for the marine iron cycle
      • Carbonate chemistry is based on MOCSY 2.0 routines (see Orr and Epitalon, 2015), by complying also with CMIP6 standards.
      • Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA)
  • High Performance Computing: performances improvements
    • Reduce number of MPI communications (suppression of redundant communications, gather multiple communications into one)
    • Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements)
    • XIOS software for IOs version 2 as default, and optionally available for restarts
  • Simplification and robustness
    • Revised structure of namelist_ref/_cfg and default reference values.
    • Lateral physics (LDF): simplification of user interface and removal of CPP keys
    • Vertical physics (ZDF) (modularity, share shear production calculation between TKE and GKS, removal of all ZDF CPP keys, removal of avmu & avmv, minimization of MPP comm.: ~15 removed)
    • Remove the split-explicit ZDF scheme for both TRA and DYN
    • Remove the acceleration of convergence
    • Generalised lbc_lnk and lbc_nfd
    • Unify mppini
    • Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns
    • MPI Message passing re coded
    • Configuration interface completely rewritten (DOM module mainly suppressed , and in place: file, or usr_def module)
  • Collaborative Development Environment
    • Access to information on NEMO wiki reorganised through portals for users/developers/System Team and complete refactoring of all wiki pages and their layout
    • Reorganisation of svn repository to be compliant with usual directory tree and facilitate building of NEMO executable
    • Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community
    • Forums created
    • NEMO public web site has been cleaned and is now much nicer (using Wordpress rather than EzP)
    • New mailing lists have been set up
    • Improvements of reliability through automatic and regular testing of the changes made in repository


Milestone: 2015 simplification

Completed 6 years ago (2017-09-29T17:41:02+02:00)

The simplification of NEMO (suppress obsolete features, rewrite to improve reliability...) has been decided and elaborated in 2014.
In 2015, a first set of actions on simplification is scheduled. It has to be done before the new 2015 developments begin, since changes related to simplification are going to be very intrusive and new developments should start from the "simplified" code.

Ticket Summary Owner Type Component
No tickets found

Closed tickets

2015 Met_Office_13 - simplification tasks
2015 CMCC - 4: simplification tasks
2015 NOC-3 - System support and Simplification work
Observation operator simplification
ln_tra_dmp / ln_tradmp
dev NOC-3 --- Non-linear free surface as default
SIMPLIF-2 / MERCATOR-9: Suppression of solvers
Dangerous default setting of ln_useCT
2016WP SIMPLIF-2:Re-writing of interface between model and configuration

Milestone: 2015 WP

Completed 6 years ago (2017-10-05T11:56:05+02:00)

List of developments scheduled in 2015 (see 2015 workplan). These developments should be done starting from the simplified version (see 2015 simplification milestone)


Ticket Summary Owner Type Component
No tickets found

Closed tickets

AGRIF does not run with north fold
2015 CONFIGMAN-2/MERCATOR-2: Merge BDY configuration tool and SIREN
2015 HPC-2 /MERCATOR-3: OpenMP
2015 AGRIF-4/MERCATOR-5: Agrif: Enable vvl and AGRIF
2015 MERCATOR-9: enable LIM3 initialisation with a netcdf file
Efficiency improvements in the OBS operator.
2015: ROBUST-9 / CNRS-11 - Robustness and Tes Cases
commit changes/bugfix/... for SIREN
commit changes/bugfix/... for SIREN
Adding warm layer and cool skin models to NEMO
iceberg (ICB) code can't restart from single (rebuilt) restart file
ice sheet/ocean coupling development branch
Merge Trusting branch into trunk prior MP2015
Reactivate Trusting on trunk prior MP2015
Remove useless bmask after free surface simplification

Milestone: 2016 WP

Completed 6 years ago (2017-12-11T15:43:30+01:00)


Ticket Summary Owner Type Component
No tickets found

Closed tickets

ROBUST-10 Evolution of NEMO CDE
Missing call to ldf_dyn in step (only relevant to time-varying eddy viscosity cases)
New development branch for 2016 fixes to Wetting and Drying
SIMPLIF-3 : Remove key_bdy macro [WP2016]
SIMPLIF-4 : MPI safe computation as a default and clean key_mpp_rep
BUG in TVD (FCT) with vvl (non linear free surface) in v3.6_stable (trunk)
SST coupling with land/sea mask
SIMPLIF-6: Aerobulk package
AttributeError: 'bool' object has no attribute 'author'
Develop simple test case enabling east west AND south north cyclic boundaries
definition problem in usr_def routines of some variables
New development branch for TOP interface
ROBUST5_CMCC 2016 development
New development branch for merging NOC 2016 developments

Milestone: 2017 WP

Completed 6 years ago (2018-01-19T14:42:31+01:00)


Ticket Summary Owner Type Component
No tickets found

Closed tickets

AGRIF-1 / Met Office-7 - Vertical grid refinement using AGRIF (2015)
Bug in the shlat lateral boundary condition in AGRIF zooms when applying a partial or no slip condition
ENHANCE-01 New website
ENHANCE-03 New Users area in Trac
undefined rdttra in tranxt.F90 in dev_merge_2016
HPC-08 — 3D lbc_lnk argument with any size for the 3rd dimension
HPC-09_Gurvan — ZDF restructuration with reduced number of lbc_lnk call
ROBUST-8_AndrewC-MPP_no_ghost development branch
ENHANCE14 dev_r8329_ENHANCE14_SAL branch development
TO DO list for the end of the 2017 merge party
Memory leak in timing code, incomplete fix
SVN mime-type for namelists to enable syntax highlighting
NOC-2_JamesH-SCO_ISF development branch
AGRIF3 Jerome-vvl
improve restart read/write in LIM3
ORCA2_SAS not restartable
Wave coupling branch - New Stokes drift profile and wind stress
AGRIF code corruption test fails in SETTE
Merge of Met Office 2017 branches
Wetting and Drying
Merge of MERCATOR 2017 branches
Merge Met Office & Mercator 2017 branches

Milestone: 2018 release-4.0

Completed 5 years ago (2019-04-04T18:54:20+02:00)

Specific milestone for 2018 to monitor selected questions related to the release of NEMO 4.0.


Ticket Summary Owner Type Component
No tickets found

Closed tickets

HPC-06(2017WP) XIOS restart read functionality
HPC-07(2017WP) Write restart file using XIOS
ROBUST-14(2017WP) Removal of configuration-dependent hardcoding from closea module in OPA
ORCA2_LIM3_PISCES crashes after 179 timesteps in dev_merge_2017
writing of iceberg restarts doesn't work with ln_rst_list=.true. in dev_merge_2017
small fix for iceberg trajectory rebuilding script (
zdf_iwm_init (zdfiwm.F90) reads from a misnamed name list
VALID-06_storkey_global validation of proto-NEMO 4.0 release in ORCA1, ORCA025 and ORCA12
Bug in bdydta for ice (3.6_STABLE and dev_merge_2017)
bug if eos10 and interactive melt activated
Reorganisation of nemogcm.F90 and mppini.F90 to better separate domain decomposition functions from the rest of the initialisation
Out of bounds error in the extended row form of lbcnfd
LDF: scale-aware setting of viscous and diffusive coefficient
pb compiling iom.F90 without key_iomput
time splitting and isf: bugs
problems compiling reference config. C1D_PAPA in the trunk
coastline value of u-, v-tau in presence of sea-ice
ln_nnogather and land suppression
Missing value in ORCA2 ouput
non reproductible NP folding
Segfault from BDY indexing and code error from fldread data load without time interpolation
Bug in traadv_fct.F90
Restoring restart ability with icebergs
Redundant logical keys in lateral diffusion for passive tracers
reactivate predefined zoom with xios2
Wraparound rows not passed in coupling fields
Bug in vertical advection with ice shelf and vector form
bug in traadv_fct.F90 in trunk
Bug in diawri.F90 (both v3.6_STABLE & trunk)
duplicated code in trd_tra_iom
Uniqueness of iceberg labels can not be guaranteed if restarting from a collated restart file
solver in ice_thd_zdf
sequential compilation with sea-ice
No vertical diffusion in Offline mode
cn_cfg variable : problem with capital letters
Improved and functional sediment module in PISCES
Trivial missing implicit bfriction in barotropic subcycle for cases other than ln_dynadv_vec
Add neuler test before reading restart in dynspg_ts
WAD bug in limiting SBC fluxes in 'dry' cells
depth[tuvw]_bounds initialised to wrong values in iom_init
Update MPP_PREP to NEMO_4.0_beta
Add deflation/chunking in REBUILD_NEMO
ln_trabbl used before to be initialised
Variable "total2sws" is used before it is defined (PISCES)
bug in case of direct sea ice assimilation
sette fails to compile
bdyvol not working
Update BDY documentation
Compilation of the SI3 component fails in non-MPP configuration
The linking of BDY code fails in a non-MPP configuration

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