NEMO 2015 workplan - Shared actions

  1. NEMO 2015 workplan - Shared actions
      1. AGRIF
        1. AGRIF-1 / Met_Office-7 - AGRIF vertical grid refinement
      2. AGRIF-2 / CNRS-7 - Investing in AGRIF expertise
      3. AGRIF-3 /MERCATOR-4 - AGRIF + time-splitting compatibility (ctnd)
      4. AGRIF-3 /MERCATOR-5 - Enable vvl and AGRIF
      5. High Performance Computing
      6. HPC-1 / CMCC-1 - Scalability with MPI-OPENMP
      7. HPC-2/ MERCATOR-3 - investigate on openMP
      8. HPC-3 / CNRS-17 - OASIS coupling between OPA and LIM/CICE
      9. Configuration Manager
        1. CONFIGMAN-1 / MERCATOR-1 - NEMO working group - Agree and test SIREN code
        2. CONFIGMAN-3 / MERCATOR-2 - Merge BDY configuration tool and SIREN
      10. System simplification
        1. SIMPLIF-1 / NOC-3 - System support and Simplification work
        2. SIMPLIF-2 / CMCC-4 - System simplification
        3. SIMPLIF-3 - System simplification
      11. Wave Coupling
        1. Wave Coupling-1 / Met Office-8 - Modifications to surface coupling …
        2. Wave Coupling-2 / INGV-1 - Implementation of the WAVE-WG 2014 results
        3. Wave Coupling-3 / INGV-2 - Definition of a configuration to test …
        4. Wave Coupling-4 / INGV-3 - Definition of wave coupling at small (coastal) …
      12. NEMO robustness
        1. ROBUST-1/MERCATOR-6 - TOP online coarsening
        2. ROBUST-2 -CNRS-7 - NEMO ready for ESMs-CMIP6: ORCA1_LIM3_PISCES
        3. ROBUST-3 / Met_Office-12 - Validation (including ORCA025/AMM12/AMM7)
        4. ROBUST-4 / MERCATOR-7 - test NEMO3.6 with global configuration
        5. ROBUST-5 / CMCC-5 - OBC with BDY for biogeochemistry
        6. ROBUST-6 / CNRS-9 - Improvment of lateral diffusion and dissipation
        7. ROBUST-7 / Met_Office-10 - Effiency improvements in OBS
        8. ROBUST-9 / CNRS-11 - Lead working Group on Tests cases
      13. GMD/ MERCATOR-8 - GMD special issue: Modelling turbulent vertical mixing …

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Action Brief description Status end 2015 From PI
AGRIF
AGRIF-1 Implement Vertical Grid Refinement Some work has taken place on this task but much work remains to be done in 2016. Less time than planned was spent on this due to time spent resolving results changes when putting the AGRIF branch back in trunk. Met Office Tim Graham
AGRIF-2 Investing in AGRIF expertise CNRS Sebastien Masson
AGRIF-3 test last development of coupling at barotropic time step and vvl adaptation with new version of agrif Agrif and split-explicit free surface is ok. Coupling is however still implemented at baroclinic level. Full coupling at barotropic time step, while more robust, requires deep changes of the time stepping organisation. This will be investigated when a new two-level time stepping will be available.
Some work has been done concerning AGRIF and VVL. It has been ensured in particular that one-way nesting and vvl (zstar coord. only) work. This capability is available in the NEMO_3.6_STABLE code with additional SETTE tests for AGRIF. Two-way nesting and vvl is postponed in 2016 as well as the possible use of ztilde coordinate.
Mercator Jerome Chanut
AGRIF-4 AGRIF + LIM3 Postponed 2016 (was waiting for AGRIF update) CNRS Clément Rousset
HPC
HPC-1 Scalability with MPI-OpenMP CMCC S. Mocavero
HPC-2 investigate on openMP MERCATOR M. Chekki
HPC-3 OASIS coupling between OPA and LIM/CICE Done in 3_6_STABLE CNRS S. Masson
Config. Manager
CONFIGMAN-1 Agree and test SIREN code working group
CONFIGMAN-2 BDY configuration tool NOC, CMCC James Harle, Stefania Ciliberti
CONFIGMAN-3 Merge BDY configuration tool and SIREN Mercator, NOC, CMCC Julien Paul, James Harle, Stefania Ciliberti
System simplification
SIMPLIF-1 Non-linear free surface as default option NOC Andrew Coward
SIMPLIF-2 free surface simplification (suppression of solvers) Will be merged in the trunk by end 2015 MERCATOR Jérôme Chanut
SIMPLIF-¾ advection/lateral diffusion Will be merged in the trunk by end 2015 CNRS
SIMPLIF-5 Configurations Offline tool written to generate Scoordinates offline in preparation for removal of domzgr from the code (Met Office) CNRS/Met Office (+all)
SIMPLIF-2 Removal of obsolete options CMCC/Met Office Dorotea Iovino/Tim? Graham
Wave coupling
WAVE-1 Surface coupling modifications for waves A branch has been created for this but several fields still need to be added to be consistent with the INGV wave branch Met Office Francois-Xavier Boquet
WAVE-2 Implementation of the WAVE-WG 2014 results INGV E. Clementi
WAVE-3 Definition of a configuration to test wave-current interactions INGV E. Clementi
WAVE-4 Definition of wave coupling at small (coastal) scale INGV M. De Dominicis
NEMO robustness
ROBUST-1 TOP online coarsening Mercator, CNRS Clement Bricaud, Coralie Perruche, Christian Ethé
ROBUST-2 NEMO ready for ESMs-CMIP6: ORCA1_LIM3_PISCES Done in 3_6_STABLE. Available through shaconemo forge project CNRS Claire Levy
ROBUST-3 Validation of NEMO3.6 (inc. ORCA025 and AMM7) Met Office Enda O'Dea, Tim Graham, Dave Storkey
ROBUST-4 test NEMO3.6 with global configurations + test new features (LIM3, VVL, time-splitting, flux form,…) Mercator Romain Bourdalle-Badie, Clement Bricaud, Jerome Chanut
ROBUST-5 OBC with BDY for biogeochemistry CMCC Tomas Lovato
ROBUST-6 Improvement of lateral diffusion and dissipation Will be merged in the trunk by end 2015 CNRS Sebastien Masson/Gurvan? Madec
ROBUST-8 Efficiency improvements in OBS Merged at end of 2015 Met Office Jennie Waters
ROBUST-9 Lead working Group on Tests cases Ongoing work CNRS Simona Flavoni
GMD Special Issue
Coupling NEMO with wave model: first step and sensitivity experiments in the Mediterranean Sea INGV E. Clementi
Atmospheric pressure in semi -enclose basin using time-splitting and filtered free surface formulation INGV P. Oddo
Split-explicit free surface and tide (Yellow Sea) CMCC D. Wang
Performance and results of the high-resolution biogeochemical model PELAGOS025 within NEMO CMCC I. Epicoco
The coupling of the flexible stoichiometric model BFM with NEMO CMCC M. Vichi
Comparison of TKE and GLS (submitted) MERCATOR G. Reffray, R. Bourdalle-Badie
A generic approach to explicit simulation of uncertainty in the NEMO ocean model Published 27 January 2015 CNRS J.-M. Brankart
PISCES-v2 : An ocean biogeochemical model for carbon and ecosystem studies Published 16 February 2015 CNRS O. Aumont
NEMOTAM: tangent and adjoint models for the ocean modelling platform NEMO (submitted) Published 29 April 2015 CNRS A. Vidard
NEMO–ICB (v1.0): interactive icebergs in the NEMO ocean model globally configured at eddy-permitting resolution Published 27 May 2015 NOC

AGRIF

AGRIF-1 / Met_Office-7 - AGRIF vertical grid refinement

Motivation: Vertical grid refinement in NEMO would be a useful tool in simulating some aspects of the ocean (e.g. overflows)
Status: Laurent Debreu has a first attempt version of this.
Main Tasks: Take Laurent's 1st attempt code and update/improve it to provide this functionality
Science Reviewer:
System Reviewer:
Deadline:
Priority: Medium
Depends on:
Principal Investigator : Daley Calvert/Tim? Graham (TBD)

AGRIF-2 / CNRS-7 - Investing in AGRIF expertise

Motivation : Hands on AGRIF for xx test cases. Gathering and sharing expertise. Towards a NEMO-AGRIF tutorial/training course.
To be elaborated with other members of the consortium (making AGRIF compatible with split-explicit time stepping, s- and z-tilde coordinates, sea-ice…)
Status :
Main tasks :
(1) use of AGRIF in coupled ocean-atmosphere and coupled oceanic configurations
(2) contribute to the shared expertise by building a tutorial/training course
(3) write a documentation of the NEMO interface to AGRIF
(4) salve the issue of AGRIF with TKE (and GLS) vertical physics at the Equator
Science Reviewer: Jerome Chanut
System Reviewer: Jerome Chanut
Deadline: end 2015
Priority: high
Depends on :
Principal Investigator : Sébastien Masson

AGRIF-3 /MERCATOR-4 - AGRIF + time-splitting compatibility (ctnd)

Motivation: Enable AGRIF and time splitting: 2nd step: coupling at barotropic level
Status : started in 2014
Main tasks : run with a regional configuration
Science Reviewer: sebastien masson <smasson@…>
System Reviewer: sebastien masson <smasson@…>
Deadline: 2015
Priority: medium
Depends on: Design of future time stepping
Principal Investigator : Jerome Chanut <jchanut@…>

AGRIF-3 /MERCATOR-5 - Enable vvl and AGRIF

Motivation: AGRIF currently works with fixed in time vertical grid
Status : not started
Main tasks :
Science Reviewer: sebastien masson <smasson@…>
System Reviewer: sebastien masson <smasson@…>
Deadline: 2015
Priority: low
Depends on:
Principal Investigator : Jerome Chanut <jchanut@…>

High Performance Computing

HPC-1 / CMCC-1 - Scalability with MPI-OPENMP

Motivation: Improve NEMO scalability.
Status : continuation of 2014 dev CMCC-1
Main tasks : extension of the hybrid OpenMP/MPI approach to the entire code
Science Reviewer:
System Reviewer:
Deadline: December 2015
Priority: HIGH
Depends on:
Principal Investigator : S. Mocavero (silvia.mocavero@…)

HPC-2/ MERCATOR-3 - investigate on openMP

Motivation: scalability.
Status : working with CMMC; waiting for CMCC report.
Main tasks :
Science Reviewer:
System Reviewer:
Deadline: December 2015
Priority: HIGH
Depends on:
Principal Investigator : Mondher Chekki <mondher.chekki@…>

HPC-3 / CNRS-17 - OASIS coupling between OPA and LIM/CICE

Motivation: Improve NEMO scalability.
Status : under development with E. Maisonnave and G. Madec
Main tasks : modify coupling interface to be able to do a coupling between OPA and LIM/CICE (through the Stand Alone Surface Module)
Science Reviewer:
System Reviewer:
Deadline: May 2015
Priority: P1
Depends on:
Principal Investigator : S. Masson (smasson@…)

Configuration Manager

CONFIGMAN-1 / MERCATOR-1 - NEMO working group - Agree and test SIREN code

Motivation: A configuration manager demonstrator (SIREN) was added to NEMO TOOLS. Some bugs were fixed this year. Now those code should be agreed and tested.
Status :
Main tasks :

  • check AGRIF and SIREN ouput compliancy
  • check use of ice/tracers/dynamics data on boundary
  • SIREN can not handle north fold. An arbitrary limit of 88°N was added. However this imit has to be tested, and may be changed

Science Reviewer: sebastien masson <smasson@…>
System Reviewer: sebastien masson <smasson@…>
Deadline: end of 2015
Priority:high
Depends on:
Principal Investigator : Julien Paul <julien.paul@…>
'

CONFIGMAN-2 / NOC-1 - BDY configuration tool

Motivation: The ability for NEMO to be configured and run as a regional model with open boundaries forced with output saved from a wider area configuration is under-used due to the difficulty of preparing suitable boundary files. This task aims to contribute to the Configuration manager shared action by providing a high-level tool capable of completing all the necessary steps.
Status :
Main tasks : To produce an open source Python tool to configure open boundary (BDY) condition files for use with NEMO v3.4 onwards by transferring data from global NEMO simulations to defined regional domains. The tool will produce tracer/ice/dynamics (including tidal boundaries from TPXO7.2) BDY files. Written in Python this tool will be ready for integration into an all encompassing 'Configuration Manager' if desired.
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : James Harle

CONFIGMAN-3 / MERCATOR-2 - Merge BDY configuration tool and SIREN

Motivation: Two different tools to create regional configuration (SIREN and BDY configuration tool) will be added to NEMO. We have to merged those tools.
Status : not started
Main tasks : Check compatibility of those tools. And try to make it work as one.
Science Reviewer: James Harle
System Reviewer: James Harle
Deadline: end of 2015
Priority: medium
Depends on:
Principal Investigator : Julien Paul <julien.paul@…>

System simplification

SIMPLIF-1 / NOC-3 - System support and Simplification work

Motivation: The need for simplifying NEMO in preparation for next generation computer architecture work has been accepted by the NEMO community. The exact details of what is to be done and the timing and order of these changes has yet to be decided. NOC expects to take an active role in this process and reserves a substantial block of its annual contribution to ensure it can respond accordingly to the consortium plans. This block also covers routine system team work to respond to user initiated tasks (bug-fixes, requests for assistance, documentation etc.).
Status :
Main tasks :
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : Andrew Coward

SIMPLIF-2 / CMCC-4 - System simplification

Motivation: CMCC will contribute to the simplification process removing obsolescent features. Specific details on what and when have yet to be worked out.
Status :
Main tasks :
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : Dorotea Iovino

SIMPLIF-3 - System simplification

Motivation: Met office will contribute to simplification process either via code cleaning or simplifying the vertical coordinates (Details to be determined)
Status :
Main tasks :
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : Dave Storkey/Tim? Graham

Wave Coupling

Wave Coupling-1 / Met Office-8 - Modifications to surface coupling required for surface waves

Motivation: Surface wave coupling will require changes to sbccpl to allow surface waves in coupled models (Action from Wave WG meeting) [BR]] Main tasks : Changes to sbccpl
System Reviewer:
Deadline:
Priority: high
Depends on: Wave Coupling-2
Principal Investigator: Francois-Xavier Boquet

Wave Coupling-2 / INGV-1 - Implementation of the WAVE-WG 2014 results

Motivation: In 2014 the Wave–WG defined a series of developments to be implemented by the WG participants in order to implement processes occurring from meso-scale to large-scale. A temporary branch hosting the surface wave components from ECMWF already exists and some modifications respect to this branch have been identified. INGV will take care of some of the developments identified
Status : Implementation of some of the identified processes has been started in 2014. To be continued in 2015
Main tasks :
- 3D Stokes drift computation will be modified according to Breivik et al., (2014) formulation. It will be a public variable to be used also in other terms (tracers and momentum advection, surface vertical velocity);
- implementation of surface vertical velocity accounting for the Stokes Drift in case of wave coupling;
- implementation of the tracers advection accounting for the 3D Stokes drift;
- implementation of the Qiao et al., (2010) formulation accounting for the enhanced vertical mixing induced by waves;
- others if agreed by the WAVE-WG.
System Reviewer:
Deadline:
Priority: high
Depends on:
Principal Investigator: Emanuela Clementi (emanuela.clementi@…)

Wave Coupling-3 / INGV-2 - Definition of a configuration to test wave-current interactions

Motivation: A proper configuration is needed in order to test the wave-current developments as agreed by the WAVE-WG
Status : To be started
Main tasks: Contribute, within the WAVE-WG, in the definition and implementation of a configuration to test the wave-current processes implemented
System Reviewer:

Deadline:
Priority:
Depends on: INGV.01 and NEMO-WAVE WG actions
Principal Investigator: Emanuela Clementi (emanuela.clementi@…)

Wave Coupling-4 / INGV-3 - Definition of wave coupling at small (coastal) scale

Motivation: According to the WAVE-WG, in order to achieve a full wave-current coupling, the small (coastal) scale processes need to be investigated
Status: To be started
Main tasks: Contribute, within the WAVE-WG, in the analysis of this issue in order to finalize the discussion started in 2014 before proceeding with any new implementation
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator: Michela De Dominicis (michela.dedominicis@…)

NEMO robustness

ROBUST-1/MERCATOR-6 - TOP online coarsening

Motivation: run online top/pisces with lower resolution than physics
Status : developped on NEMO_3.4 / run with ORCA025
Main tasks :
-bug correction for output coarsening ( already in NEMO 3.6 )
-test output coarsening with ORCA025
-phasing new routines for TOP/PISCES and OPA from 3.4 to 3.6
-adaptation to VVL
-time degradation
Science Reviewer: Gurvan Madec <gm@…>
System Reviewer: Gurvan Madec <gm@…>
Deadline: april 2015
Priority: high
Depends on:
Principal Investigator : Clement Bricaud <cbricaud@…>,Christian Ethé <Christian.Ethe@…>, Coralie Perruche <cperruche@…>

ROBUST-2 -CNRS-7 - NEMO ready for ESMs-CMIP6: ORCA1_LIM3_PISCES

Motivation: Set-up run and validate the ORCA1_LIM3_PISCES configuration on nemo_v3.6_STABLE release to be ready for CMIP6
Status : Started in 2014. First control run available
Main tasks : Finalize physical and numerical choices for this configuration. Run and validate the forced reference experiments. Distribute this shared configuration on a specific svn/dods project (separate from NEMO reference)
Science Reviewer:
System Reviewer:
Deadline: May 2015
Priority: 1 (= for CMIP6)
Depends on:
Principal Investigator : Claire Lévy

ROBUST-3 / Met_Office-12 - Validation (including ORCA025/AMM12/AMM7)

Motivation: Model configurations need to be validated before the release of the model.
Status: Main Tasks:

  • Upgrading configs to new model version (after merge party)
  • Assessment of changes to output
  • SETTE testing at latest revision
  • Finding & fixing causes of any issues Science Reviewer: N/A
    System Reviewer: N/A
    Deadline:
    Priority:
    Depends on:
    Principal Investigator : Tim Graham/Dave? Storkey/Enda? O'Dea

ROBUST-4 / MERCATOR-7 - test NEMO3.6 with global configuration

Motivation: Model configurations need to be validated before the release of the model.
Status: ORCA025_LIM2 with filtread free surface or time splitting is already running at Mercator
Main Tasks: Test and validation with ORCA025 of:

-LIM2 vs LIM3
-GLS vs TKE
-time-splitting vs filtred free surface
-vector form vs UBS for momentum advection
-run ORCA025 with Z*
-online coarsening
-run ORCA12 with time-splitting/LIM2/GLS/UBS?
-online coarsening

Science Reviewer: Martin Vancoppenolle <martin.vancoppenolle@…>,"Andrew C. Coward" <acc@…>,Gurvan Madec <Gurvan.Madec@…>
System Reviewer: N/A
Deadline:
Priority: medium
Depends on: implementation of online coarsening
Principal Investigator : Clement Bricaud <cbricaud@…>,Romain Bourdallé-Badie <rbourdal@…>, Jerome Chanut <jchanut@…>

ROBUST-5 / CMCC-5 - OBC with BDY for biogeochemistry

Motivation: finalize the treatment of boundary conditions for TOP
Status : continuation
Main tasks : use BDY with biogeochemistry using the structures implemented in 2014 development.
Science Reviewer: D. Storkey
System Reviewer: C. Ethé
Deadline: March 2015
Priority: HIGH
Depends on:
Principal Investigator : Tomas Lovato

ROBUST-6 / CNRS-9 - Improvment of lateral diffusion and dissipation

Motivation: simplify and improve the lateral diffusion and dissipation in NEMO/OPA
Status : Continuation
Main tasks :

  • Simplification:
    • change the way the eddy diffusivity and viscosity are specified and controlled by the user
  • Improvements:
    • introduce Beckers et al. (2000) compact stencil in the cross-isoneutral direction in triads formalism
    • introduce in both iso-neutral operator the Method of Stabilizing Correction (Lemarié et al. (2012)
    • implement bilaplacian iso-neutral operator (Lemarié et al. (2012)
      Science Reviewer:
      System Reviewer:
      Deadline: May 2015
      Priority: Medium
      Depends on: N/A
      Principal Investigator : Gurvan Madec/Sebastien? Masson

ROBUST-7 / Met_Office-10 - Effiency improvements in OBS

Motivation: OBS operator needs to be more efficient for future use in high resolution models (e.g. ORCA12) Status: Main Tasks: Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : Jennie Waters

ROBUST-9 / CNRS-11 - Lead working Group on Tests cases

Motivation: There are several motivations to define a suite of standard test-cases for NEMO (e.g. for pedagogical purpose and/or for demonstrating the benefit of new features and/or for illustrating the effect of a numerical scheme). This work will be done in throughout a Working Group. The purpose of the Working Group is to (i) specify the expected outcome of standard test-cases in NEMO and (ii) to define how standard test-cases should be distributed within NEMO. There will be interactions with Configuration Manager Working Group to decide how input files (bathymetry, coordinates,…) will be given, and how they will be maintained. In 2015, this new working group will need to be started (list of members to be fianlised during Developer’s Committee 2014).
Status : Starting
Main tasks :
Science Reviewer:
System Reviewer:
Deadline:
Priority: P2 (2nd semester 2015)
Depends on: Simplification, Configuration Manager…
Principal Investigator : Simona Flavoni

GMD/ MERCATOR-8 - GMD special issue: Modelling turbulent vertical mixing sensitivity using a 1-D version of NEMOC

Motivation: comparison of TKE and GLS
Status : submitted, in revision
Main tasks : corrections
Principal Investigator : Guillaume Reffray <greffray@…>

Last modified 4 years ago Last modified on 2016-02-18T15:53:41+01:00