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NEMO 2016 workplan - Shared actions

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Inputs from working groups:

Summary of Shared Actions:

Action Brief description Status end 2016 Institution PI
AGRIF
AGRIF-1 Continue vertical grid refinement from 2015 Met Office Tim Graham
AGRIF-2 AGRIF + LIM3 CNRS Clément Rousset
AGRIF-3 AGRIF + VVL (2 way nesting) Mercator Océan Jérôme Chanut
HPC
HPC-1 Suppress Global Comms (mpp_sum etc)* CMCC/Met Office Silvia Mocavero/Tim? Graham
HPC-2 Gather communications* Barcelona Miguel Castrillo
HPC-3 Suppress useless comms* Met Office Tim Graham
HPC-4 Scalability with MPI-OPENMP CMCC Silvia Mocavero
HPC-5 Implement larger haloes NERC Andrew Coward
Config. Manager
CONFIGMAN-1 SIREN improvement and robustness MERCATOR julien PAUL
CONFIGMAN-2 BDY tool developpement and tests NERC/CMCC james HARLE, stefania CILIBERTI
System simplification
SIMPLIF-1 Simplification of vertical diffusion CNRS Gurvan Madec
SIMPLIF-2 Simplification of configurations, introduction of user-defined module CNRS Simona Flavoni
Wave coupling
WAVE-1 Improvements in wave-current interaction processes implementation INGV Emanuela Clementi
WAVE-2 Definition of wave-current interaction processes at small (coastal) scale INGV Emanuela Clementi
NEMO robustness
ROBUST-1 Integration of the seabass configuration as a test case CNRS Pierre-Antoine Bouttier
ROBUST-2 Improving EEN scheme for partial steps Met Office Mike Bell
ROBUST-3 Academic test case in the system CNRS Simona Flavoni
ROBUST-4 Passive tracers run offline with variable volume CNRS Christian Ethé
ROBUST-5 Revisiting TOP interface CNRS Christian Ethé
ROBUST-6 Continuous integration tool ('Trusting') CNRS Nicolas Martin
ROBUST-7 BDY for nested limited area models CMCC Stefania Ciliberti
ROBUST-8 Improve split-explicit free surface Mercator Océan Jérôme Chanut
ROBUST-9 test on ORCA025/ORCA12 Mercator Océan Clement Bricaud / Romain Bourdalle-Badie
GMD Special Issue

AGRIF

AGRIF-1 / Met Office - Increased vertical resolution with AGRIF

Motivation: Vertical grid refinement in NEMO would be a useful tool in simulating some aspects of the ocean (e.g. overflows)
Status: Started in 2015 but much more work to do
Main Tasks:
Science Reviewer:
System Reviewer:
Deadline:
Priority: Medium
Depends on:
Principal Investigator : Tim Graham

AGRIF-2 / CNRS - Assessment of LIM3 with AGRIF

Motivation: enable the use of AGRIF with LIM3 since LIM3 is the reference sea ice model in NEMO and LIM2 will soon be removed
Status: Not yet started in 2015
Main Tasks: AGRIF already works with LIM2, so the strategy here will be to adapt what is done in LIM2 to LIM3.
Science Reviewer:
System Reviewer:
Deadline: end of 2016
Priority: High
Depends on:
Principal Investigator : Clément Rousset

AGRIF-3 / Mercator Océan - Agrif + vvl (two way nesting)

Motivation: Enable the use of agrif with temporally varying vertical grid (e.g. with zstar or ztilde coordinates)
Status: Started in 2015. One way nesting is ok, two way nesting needs to be finalized.
Main Tasks:
Science Reviewer:
System Reviewer:
Deadline:
Priority: High
Depends on:
Principal Investigator : Jérôme Chanut

HPC

HPC-1 / CMCC/Met Office - Suppress global communications

Motivation: Removing global communications could help improve the speed of NEMO
Status: Not started
Main Tasks: Silvia Mocavero to investigate which communications could be safely removed. Tim Graham to look at a more efficient implementation of functionality in stp_ctl.
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : Silvia Mocavero/Tim? Graham

HPC-2 / Barcelona - Gather communications

Motivation: Grouping communications (lbc_lnk) together is more efficient than several separate lbc_lnk calls.

Status: lbc_lnk_multi in 3.6
Main Tasks: Extend functionality of lbc_lnk_multi to 3D (or 4D variables). Find calls to lbc_lnk that can be replaced with lbc_lnk_multi.
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : Miguel Castrillo

HPC-3 / Barcelona - Suppress useless communications

Motivation: Suppress unnecessary calls to lbc_lnk.


Status:
Main Tasks: Use a script to search for and test impact of removing lbc_lnk calls from the model code. Determine whether communications used for diagnostic purposes can be suppressed.
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : Tim Graham

HPC-4 / CMCC - Scalability with MPI-OPENMP

Motivation: Improving NEMO scalability.


Status: continuation of 2015 dev CMCC-1
Main Tasks: 1. the activity started at the end of 2013 with the analysis of three OpenMP approaches (implemented using “mini-apps”) on several multicore architectures; the second step was the implementation of the hybrid version of the GYRE configuration using the best OpenMP approach. Results in terms of scalability were not so good. Thus, the porting and the analysis of the hybrid version (using “mini-apps”) on many core architectures (e.g. Xeon Phi) is needed, before extending the hybrid OpenMP/MPI approach to the entire code, in order to justify the effort of the development. This analysis is carrying out in 2015. The extension of the hybrid implementation on the entire code will depend on the results of this analysis. 2. analysis of scalability improvement using MPI3 new communications (e.g. collective neighbours communications), instead of point to point communications
Science Reviewer:
System Reviewer:
Deadline:
Priority: HIGH
Depends on: results of the same action in 2015
Principal Investigator : Silvia Mocavero

HPC-5 / NERC - Implement larger haloes

Motivation: Improving NEMO scalability.


Status: New implementation - old idea
Main Tasks: Investigate the benefits of using larger halo to reduce the communication frequency and hence improve performance and scalability. This is likely to be most influential in the barotropic time-splitting where it should be possible to emulate earlier solutions for the iterative solvers. Extension to the rest of the code will be considered subject to an impact assessment.
Science Reviewer:
System Reviewer:
Deadline:
Priority: HIGH
Depends on:
Principal Investigator : Andrew Coward

SIMPLIFICATION

SIMPLIF-1 / CNRS - Simplification of vertical diffusion

Motivation: Introduce a vertical physics manager that allows to save MPP communications

Status: Already started
Main Tasks:
Science Reviewer:
System Reviewer:
Deadline:
Priority: High
Depends on:
Principal Investigator : Gurvan Madec

SIMPLIF-2 / CNRS - Simplification of configurations, introduction of user-defined module

Motivation:  Remove all hard coded reference to configurations. we want that : a configuration will be defined by reading external files (coordinates, bathymetry and mesh_mask, initial state (not analytical), input and forcing files, open boundary conditions)

Status: New implementation / the idea of the work is already started inside the Working group Robustness and Test cases.
Main Tasks:

  • remove all hard coded configuration (if orca….)
  • all files defining the configuration are read (put flag in namelist: if read read file, if not call user_module)
  • implement GYRE like the ONLY standard example of configuration that does not read files
  • create the "user_defined_module.F90" in NEMO code (users_defined_sbc, users_defined_forcing, users_defined_bdy, users_defined_bathymetry, …)

Science Reviewer:
System Reviewer:
Deadline:
Priority: High
Depends on:
Principal Investigator : Simona Flavoni

Configuration Manager

ConfigMan-1 / MERCATOR - SIREN improvement and robustness

Motivation:

  • test SIREN code (working group members and maybe some external users)
  • extract from NEMO the meshmask creation (Mercator-Océan)
  • main program (python) to manage all SIREN codes (Mercator-Océan)
  • improve documentation readibility, and add tutorial (Mercator-Océan)


Status:
Main Tasks:
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : julien PAUL

ConfigMan-2 / NERC/CMCC - BDY tool developpement and tests

Motivation:

  • finish last improvement of the BDY tool and add some documentation (NERC)
  • test BDY tool (CMCC)


Status:
Main Tasks:
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator : james HARLE, stefania CILIBERTI

Wave Coupling

WAVE-1 / INGV - Improvements in wave-current interaction processes implementation ===

Motivation: INGV is responsible for the WAVE-WG and will continue improving the wave-current interaction processes implementation according to the WG needs.
Status : Implementation of some of the identified processes has been started in 2014 and 2015. To be continued in 2016
Main tasks : Continue the implementation of already defined wave-current processes, if not completed in previous year. Meeting organization with the WAVE-WG to discuss further issues to be investigated and implemented:

  • Vertical mixing enhancement due to wave breaking;
  • Contribute to the discussion on implementation of Langmuir circulation;
  • Contribute to the discussion on wave-sea ice coupling; ;
  • others if agreed by the WAVE-WG.

Science Reviewer: Rachid Benshila
System Reviewer: Rachid Benshila
Deadline:
Priority: high
Depends on:
Principal Investigator: Emanuela Clementi (emanuela.clementi@…)

WAVE-2 / INGV - Definition of wave-current interaction processes 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 continued in 2016
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: Rachid Benshila
System Reviewer: Rachid Benshila
Deadline:
Priority:
Depends on:
Principal Investigator: Emanuela Clementi (emanuela.clementi@…)

ROBUSTNESS

ROBUSTNESS-1 / CNRS - Integration of the SEABASS configuration as a test case

Motivation: SEABASS is the reference configuration for Data Assimilation, included in the NEMO v3.4_STABLE version. Various data assimilation experiments have been done with this configuration, with various data assimilation systems (e.g. Cosme et al, 2011, Bouttier et al. 2014, Yin et al., 2014). In this context, this configuration appears to be useful for data assimilation users, to couple their own DA system on NEMO and compare their results with thgose obtained on this configuration. SEABASS is also easy to take in hand. Also, it allows to update the configuration status to the future version of NEMO. For these reasons, this configuration is a relevant test case for Data Assimilation.
Status:
Main Tasks:
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator: Pierre-Antoine Bouttier

ROBUSTNESS-2 / Met Office - Improvements to EEN scheme with partial steps

Motivation: Following investigative work by Nicolas Ducousso it became clear that the EEN scheme in NEMO did not perform as expected in idealised test cases. Although a fix was implemented that improved the performance in idealised test cases the performance in realistic simulations (e.g. ORCA025) is worse. It is not clear that the new or old formulation is correct for the case of sloping bathymetry and partial steps.


Status:
Main Tasks:
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:

ROBUSTNESS-3 / CNRS - Academic test cases in the system

Motivation: Implementation 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)
Status: started in 2015
Main Tasks: after the structure of user_defined module is created in the code (see SIMPLIF-2 CNRS), a list of test cases will be implemented (suggestion one test case related to the main development of the year for each institution).
The working group on Test cases and robustness will decide the structure fo the implementation in NEMO of test cases (work already started, with a template of equatorial box in 2015 branch).

Science Reviewer: Gurvan Madec
System Reviewer:
Deadline:
Priority: High
Depends on: SIMPLIF-2 (CNRS)
Principal Investigator: Simona Flavoni

ROBUSTNESS-4 / CNRS - Passive tracers run offline with vvl

Motivation: Add missing pieces of code to be able to run offline component with vvl
Status: Started in 2015 ; to be improved
Main Tasks:

(1) run a forced simulation ORCA2(1)-LIM2(3) and output variables needed for linear free surface, especially the changing vertical grid in time ( already done )
(2) Rewrite the Offline module to take into account the changing grid in time
Science Reviewer:
Gurvan Madec
System Reviewer:
Deadline:
Priority: High
Depends on:
Principal Investigator: Christian Ethé

ROBUSTNESS-5 / CNRS - Revisiting TOP interface

Motivation: Some aspects of TOP interface need to be improved
Status:
Main Tasks:

(1) move the number of passive tracers from the code to the namelist
(2) generalisation of the work done at CMCC on boundary conditions to others models in the system ( PISCES, CFC, C14b )
Science Reviewer:
Olivier Aumont
System Reviewer:
Deadline:
Priority: Low
Depends on:
Principal Investigator: Christian Ethé

ROBUSTNESS-8 / Mercator Océan - Improve split-explicit free surface

Motivation: There are several aspects that need to be investigated concerning the robustness of current split-explicit algorithm:

  • Tracer conservation issues (all time splitting options do not ensure global and local tracer conservation).
  • Missing correction terms in the barotropic equations relative to internal pressure gradients. This would reduce mode splitting error, hence improve stability.
  • Work on the stability of barotropic time stepping (based on INRIA's work) to possibly remove time filtering of barotropic variables. This would limit the temporal dissipation and greatly ease online coupling of nested domains at barotropic level (with AGRIF).

Status:
Main Tasks:
Science Reviewer:
System Reviewer:
Deadline:
Priority:
Depends on:
Principal Investigator: Jérôme Chanut