Announcement 4.0.beta NEMO release

Last edition on 2018-07-11 14:47 CEST by clevy

11 July 2018
The new 4.0.beta release of NEMO is now available for beta testing. The official 4.0 release is scheduled for end 2018. The users and projects willing to make preliminary tests and contribute to the reliability of the future 4.0 release are very welcome to start testing this new 4.0.beta version. This page gathers all the information needed for a quick start, and all feedbacks are welcome, see below.

Download the nemo 4.0.beta release

The nemo 4.0 beta release is available in the repository starting at revision 9925.
To download nemo 4.0.beta:

svn co

Changes in repository and building executable

To make it compliant to usual directory tree, and to facilitate building NEMO executable, there has been some changes in the repository layout:

To build NEMO executable in this release:
Changes to quickstart page to be added here Following the changes in repository layout, once code is downloaded:

cd trunk
./makenemo [options] # as usual, see wiki page below

Quickstart wiki page

Important notice on XIOS revision

The official and supported version of XIOS is XIOS 2.5, which should be used from now on.

svn co ​ xios-2.5 

It has been tested and works with NEMO reference configurations, but if problems for now, try using XIOS 2.0 before requesting help through the XIOS users mailing list.

Status of the 4.0 beta release

This newly build beta release has been widely tested before this announcement:

  • All the reference configuration sucessfully complete the so-called SETTE tests: each reference configuration is running fine, is restartable (running in one step or with a restart gives identical results) and reproducible (identical results with two different domain decomposition) with optimised compiler options, and in debug mode
  • All the test cases give correct results
  • Some longer runs on most of the Reference Configurations show satisfactory scientific results.

Where to find inputs for reference configurations in 4.0 beta release?

Input files for reference configurations in 4.0 beta release

Release notes

  • 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 particulart 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 lability scheme, while the former Kriest parameterisation 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 namlist_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 faciltate 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 Word Press? rather than EzP)
    • New mailing lists have been set up
    • Improvements of reliability through automatic and regular testing of the changes made in repository

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Last modified 5 days ago Last modified on 2018-07-11T14:47:37+02:00

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