Version release-4.0

No date set

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: domain_cfg.nc 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

Milestones

Milestone: 2015 simplification

Completed 14 months 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

#1447
2015 Met_Office_13 - simplification tasks
#1456
2015 CMCC - 4: simplification tasks
#1457
2015 NOC-3 - System support and Simplification work
#1468
Observation operator simplification
#1526
ln_tra_dmp / ln_tradmp
#1613
dev NOC-3 --- Non-linear free surface as default
#1620
SIMPLIF-2 / MERCATOR-9: Suppression of solvers
#1687
Dangerous default setting of ln_useCT
#1692
2016WP SIMPLIF-2:Re-writing of interface between model and configuration

Milestone: 2015 WP

Completed 14 months 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)

wiki:2015WP

Ticket Summary Owner Type Component
No tickets found

Closed tickets

#1376
AGRIF does not run with north fold
#1450
2015 CONFIGMAN-2/MERCATOR-2: Merge BDY configuration tool and SIREN
#1451
2015 HPC-2 /MERCATOR-3: OpenMP
#1453
2015 AGRIF-4/MERCATOR-5: Agrif: Enable vvl and AGRIF
#1455
2015 MERCATOR-9: enable LIM3 initialisation with a netcdf file
#1464
Efficiency improvements in the OBS operator.
#1469
2015: ROBUST-9 / CNRS-11 - Robustness and Tes Cases
#1580
commit changes/bugfix/... for SIREN
#1581
commit changes/bugfix/... for SIREN
#1586
Adding warm layer and cool skin models to NEMO
#1590
iceberg (ICB) code can't restart from single (rebuilt) restart file
#1611
ice sheet/ocean coupling development branch
#1631
Merge Trusting branch into trunk prior MP2015
#1639
Reactivate Trusting on trunk prior MP2015
#1648
Remove useless bmask after free surface simplification

Milestone: 2016 WP

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

wiki:2016WP

Ticket Summary Owner Type Component
No tickets found

Closed tickets

#1679
ROBUST-10 Evolution of NEMO CDE
#1691
Missing call to ldf_dyn in step (only relevant to time-varying eddy viscosity cases)
#1701
New development branch for 2016 fixes to Wetting and Drying
#1729
SIMPLIF-3 : Remove key_bdy macro [WP2016]
#1730
SIMPLIF-4 : MPI safe computation as a default and clean key_mpp_rep
#1742
BUG in TVD (FCT) with vvl (non linear free surface) in v3.6_stable (trunk)
#1743
SST coupling with land/sea mask
#1751
SIMPLIF-6: Aerobulk package
#1756
AttributeError: 'bool' object has no attribute 'author'
#1761
Develop simple test case enabling east west AND south north cyclic boundaries
#1764
definition problem in usr_def routines of some variables
#1782
New development branch for TOP interface
#1783
ROBUST5_CMCC 2016 development
#1802
New development branch for merging NOC 2016 developments
#1811
dev_merge_2016

Milestone: 2017 WP

Completed 10 months ago (2018-01-19T14:42:31+01:00)

wiki:2017WP

Ticket Summary Owner Type Component
No tickets found

Closed tickets

#1458
AGRIF-1 / Met Office-7 - Vertical grid refinement using AGRIF (2015)
#1684
Bug in the shlat lateral boundary condition in AGRIF zooms when applying a partial or no slip condition
#1814
ENHANCE-01 New nemo-ocean.eu website
#1815
ENHANCE-03 New Users area in Trac
#1828
undefined rdttra in tranxt.F90 in dev_merge_2016
#1880
HPC-08 — 3D lbc_lnk argument with any size for the 3rd dimension
#1883
HPC-09_Gurvan — ZDF restructuration with reduced number of lbc_lnk call
#1896
CONFIGMAN-1/SIREN
#1897
CONFIGMAN-2/SIREN
#1898
CONFIGMAN-3/SIREN
#1915
ROBUST-8_AndrewC-MPP_no_ghost development branch
#1916
ROBUST 10 Unify MPPINI
#1926
ENHANCE14 dev_r8329_ENHANCE14_SAL branch development
#1941
TO DO list for the end of the 2017 merge party
#1942
Memory leak in timing code, incomplete fix
#1948
SVN mime-type for namelists to enable syntax highlighting
#1955
NOC-2_JamesH-SCO_ISF development branch
#1965
AGRIF3 Jerome-vvl
#1976
improve restart read/write in LIM3
#1977
ORCA2_SAS not restartable
#1980
Wave coupling branch - New Stokes drift profile and wind stress
#1988
AGRIF code corruption test fails in SETTE
#1990
Merge of Met Office 2017 branches
#1992
Wetting and Drying
#1993
Merge of MERCATOR 2017 branches
#1996
Merge Met Office & Mercator 2017 branches

Milestone: 2018 release-4.0

5 months late (2018-07-01T02:00:00+02:00)

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

Ticket Summary Owner Type Component
#1911 ENHANCE-04(2017WP) — MLF and RK3 time stepping gm Task OCE
#2010 HPC-03_Mocavero_globcomm francesca Task OCE
#2017 AGRIF-03_jchanut-TOOLS jchanut Task AGRIF
#2024 VALID-01_cbricaud_HR cbricaud Task OCE
#2025 ROBUST-06_Andrew-reporting acc Task OCE
#2026 VALID-10_GeorgeN-evalOSMOSIS agn Task OCE
#2030 VALID-06_storkey_global validation of proto-NEMO 4.0 release in ORCA1, ORCA025 and ORCA12 davestorkey Task misc.
#2049 VALID-04_SFlavoni_Overflow_Lock flavoni Task OCE
#2059 VALID-02_smasson_regional_agrif smasson Task OCE
#2060 VALID-11_cethe_TOP_Offline cetlod Task OCE
#2095 testing ideas for re-ordering loops to improve HPC performance mikebell Enhancement OCE
#2100 Missing value in ORCA2 ouput Defect OCE
#2135 Memory Bug requries compilation flag to zero all arrays to overcome in AMM15 systeam Bug TOP
#2138 key_nemocice_decomp still needed? systeam Enhancement LBC
#2154 WAD bug in limiting SBC fluxes in 'dry' cells systeam Bug SBC

Closed tickets

#1953
HPC-06(2017WP) XIOS restart read functionality
#1962
HPC-07(2017WP) Write restart file using XIOS
#2006
ORCA2_LIM3_PISCES crashes after 179 timesteps in dev_merge_2017
#2007
writing of iceberg restarts doesn't work with ln_rst_list=.true. in dev_merge_2017
#2008
small fix for iceberg trajectory rebuilding script (icb_pp.py)
#2013
VALID-09_Lovato_TestWave_MedSea
#2014
VALID-08_Drudi_Wave_ORCA2
#2027
zdf_iwm_init (zdfiwm.F90) reads from a misnamed name list
#2028
VALID-07_odea-AMM
#2031
AGRIF-02_crousset-LIM3
#2048
VALID-03_SFlavoni_global_configuration
#2061
ROBUST-01_rbourdal_C1D
#2063
Bug in bdydta for ice (3.6_STABLE and dev_merge_2017)
#2066
bug if eos10 and interactive melt activated
#2070
Reorganisation of nemogcm.F90 and mppini.F90 to better separate domain decomposition functions from the rest of the initialisation
#2074
Out of bounds error in the extended row form of lbcnfd
#2075
LDF: scale-aware setting of viscous and diffusive coefficient
#2079
pb compiling iom.F90 without key_iomput
#2081
time splitting and isf: bugs
#2087
problems compiling reference config. C1D_PAPA in the trunk
#2096
coastline value of u-, v-tau in presence of sea-ice
#2099
ln_nnogather and land suppression
#2101
non reproductible NP folding
#2103
Segfault from BDY indexing and code error from fldread data load without time interpolation
#2110
Bug in traadv_fct.F90
#2113
Restoring restart ability with icebergs
#2114
Redundant logical keys in lateral diffusion for passive tracers
#2115
reactivate predefined zoom with xios2
#2116
Wraparound rows not passed in coupling fields
#2120
Bug in vertical advection with ice shelf and vector form
#2122
bug in traadv_fct.F90 in trunk
#2123
Bug in diawri.F90 (both v3.6_STABLE & trunk)
#2125
duplicated code in trd_tra_iom
#2128
Uniqueness of iceberg labels can not be guaranteed if restarting from a collated restart file
#2139
solver in ice_thd_zdf
#2141
sequential compilation with sea-ice
#2144
No vertical diffusion in Offline mode
#2145
cn_cfg variable : problem with capital letters
#2146
Improved and functional sediment module in PISCES
#2149
Trivial missing implicit bfriction in barotropic subcycle for cases other than ln_dynadv_vec
#2151
Add neuler test before reading restart in dynspg_ts

Milestone: 2018 WP

Due in 7 weeks (2019-01-01T01:00:00+01:00)

wiki:2018WP

Ticket Summary Owner Type Component
#1426 ROBUST-01(2015WP)/MERCATOR-6 online coarsening cbricaud Task OCE
#1943 HPC-02(2017WP)_Francesca Development of the NEMO hybrid parallel version based on MPI/OpenMP francesca Task OCE
#1971 with new equation of state (TEOS10) input files in T and S need to be changed, according to the new equation of state (TEOS10) clevy Defect OCE
#2000 ROBUST-14(2017WP) Removal of configuration-dependent hardcoding from closea module in OPA davestorkey Task OCE
#2012 INGV-01_CLementi_AddWaveDiag emanuelaclementi Enhancement OCE
#2015 ENHANCE-11 Repository cleaning nicolasmartin Task OCE
#2016 ENHANCE-10 Trusting-SETTE cooperation nicolasmartin Task OCE
#2019 ENHANCE-03_jchanut-ZTILDE jchanut Task OCE
#2020 ENHANCE-12_Yevgeny-Icewaves acc Task OCE
#2021 HPC-05_AndrewC-extendedhaloes acc Task OCE
#2033 SEAICE-02_crousset_validation_aEVP clem Task OCE
#2034 SEAICE-03_crousset_validation_landfast clem Task OCE
#2035 SEAICE-04_crousset_evaluation_UM5vsPRATHER clem Task OCE
#2036 SEAICE-05_crousset_coupled_interface clem Task OCE
#2037 ROBUST-05_clevy_shaconemo_future clevy Task env
#2039 HPC-08_Mixed_precision_study-8.1_Assessment mcastril Task OCE
#2040 HPC-08_Mixed_precision_study-8.2_Implementation mcastril Task OCE
#2042 ENHANCE-05_Gurvan-Vertical_Advection acc Task OCE
#2044 ENHANCE-09_Gurvan-GEOMETRIC gm Task OCE
#2046 PUBLI-03_SFlavoni-advectionscheme-analysis flavoni Task OCE
#2053 ENHANCE-13_Olivier-Vertical_Sinking aumont Task OCE
#2054 ENHANCE-07_crousset_LIM3adv_valorisation clem Task OCE
#2055 ENHANCE-14_cethe_PISCES_LBC cetlod Task OCE
#2056 PUBLI-02_nicolas_Project_Bibliography nicolasmartin Task OCE
#2111 CMCC-01_sciliberti_BDYModel sciliberti Task BDY
#2112 CMCC-02_sciliberti_BDYTool sciliberti Task tools
#2133 HPC-09_Maisonnave-ATOS-ESIWACE emalod Task LBC
#2147 VALID-12_CLEVY_CoupledInterface clevy Task SBC

Closed tickets

#2047
ROBUST-07_SFlavoni-Notebook-testcases
#2089
NESTING TOOLS AGRIF: bathymetry connection done even if open boundary lies over land

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