Articles | Volume 15, issue 4
https://doi.org/10.5194/gmd-15-1567-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Special issue:
https://doi.org/10.5194/gmd-15-1567-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Development and technical paper
| 
22 Feb 2022
Development and technical paper |
| 22 Feb 2022
Improving ocean modeling software NEMO 4.0 benchmarking and communication efficiency
Gaston Irrmann
CORRESPONDING AUTHOR
LOCEAN-IPSL, Sorbonne Universités (UPMC)/IRD/CNRS/MNHN, UMR7159, Paris, France
CEPP – Center for Excellence in Performance Programming, Atos, 35700 Rennes, France
Sébastien Masson
LOCEAN-IPSL, Sorbonne Universités (UPMC)/IRD/CNRS/MNHN, UMR7159, Paris, France
Éric Maisonnave
CERFACS/CNRS, CECI, Toulouse, France
David Guibert
CEPP – Center for Excellence in Performance Programming, Atos, 35700 Rennes, France
Erwan Raffin
CEPP – Center for Excellence in Performance Programming, Atos, 35700 Rennes, France
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Andreas Müller, Willem Deconinck, Christian Kühnlein, Gianmarco Mengaldo, Michael Lange, Nils Wedi, Peter Bauer, Piotr K. Smolarkiewicz, Michail Diamantakis, Sarah-Jane Lock, Mats Hamrud, Sami Saarinen, George Mozdzynski, Daniel Thiemert, Michael Glinton, Pierre Bénard, Fabrice Voitus, Charles Colavolpe, Philippe Marguinaud, Yongjun Zheng, Joris Van Bever, Daan Degrauwe, Geert Smet, Piet Termonia, Kristian P. Nielsen, Bent H. Sass, Jacob W. Poulsen, Per Berg, Carlos Osuna, Oliver Fuhrer, Valentin Clement, Michael Baldauf, Mike Gillard, Joanna Szmelter, Enda O'Brien, Alastair McKinstry, Oisín Robinson, Parijat Shukla, Michael Lysaght, Michał Kulczewski, Milosz Ciznicki, Wojciech Piątek, Sebastian Ciesielski, Marek Błażewicz, Krzysztof Kurowski, Marcin Procyk, Pawel Spychala, Bartosz Bosak, Zbigniew P. Piotrowski, Andrzej Wyszogrodzki, Erwan Raffin, Cyril Mazauric, David Guibert, Louis Douriez, Xavier Vigouroux, Alan Gray, Peter Messmer, Alexander J. Macfaden, and Nick New
Geosci. Model Dev., 12, 4425–4441, https://doi.org/10.5194/gmd-12-4425-2019, https://doi.org/10.5194/gmd-12-4425-2019, 2019
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This paper presents an overview of the ESCAPE project. Dwarfs (key patterns in terms of computation and communication) are identified in weather prediction models. They are optimised for different hardware architectures. New algorithms are developed that are specifically designed for better energy efficiency and improved portability through domain-specific languages. Different numerical techniques are compared in terms of energy efficiency and performance for a variety of computing technologies.
C. Rousset, M. Vancoppenolle, G. Madec, T. Fichefet, S. Flavoni, A. Barthélemy, R. Benshila, J. Chanut, C. Levy, S. Masson, and F. Vivier
Geosci. Model Dev., 8, 2991–3005, https://doi.org/10.5194/gmd-8-2991-2015, https://doi.org/10.5194/gmd-8-2991-2015, 2015
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LIM3.6 presented in this paper is the last release of the Louvain-la-Neuve sea ice model, and will be used for the next climate model intercomparison project (CMIP6). The model's robustness, versatility and sophistication have been improved.
Related subject area
Oceanography
Barotropic tides in MPAS-Ocean (E3SM V2): impact of ice shelf cavities
Using the two-way nesting technique AGRIF with MARS3D V11.2 to improve hydrodynamics and estimate environmental indicators
Multidecadal and climatological surface current simulations for the southwestern Indian Ocean at 1∕50° resolution
The tidal effects in the Finite-volumE Sea ice–Ocean Model (FESOM2.1): a comparison between parameterised tidal mixing and explicit tidal forcing
HIDRA2: deep-learning ensemble sea level and storm tide forecasting in the presence of seiches – the case of the northern Adriatic
Moana Ocean Hindcast – a > 25-year simulation for New Zealand waters using the Regional Ocean Modeling System (ROMS) v3.9 model
A nonhydrostatic oceanic regional model, ORCTM v1, for internal solitary wave simulation
How does 4DVar data assimilation affect the vertical representation of mesoscale eddies? A case study with observing system simulation experiments (OSSEs) using ROMS v3.9
An ensemble Kalman filter-based ocean data assimilation system improved by adaptive observation error inflation (AOEI)
GULF18, a high-resolution NEMO-based tidal ocean model of the Arabian/Persian Gulf
The Baltic Sea Model Intercomparison Project (BMIP) – a platform for model development, evaluation, and uncertainty assessment
An ensemble Kalman filter system with the Stony Brook Parallel Ocean Model v1.0
Wind work at the air-sea interface: a modeling study in anticipation of future space missions
Development and validation of a global 1/32° surface wave-tide-circulation coupled ocean model: FIO-COM32
The 3D biogeochemical marine mercury cycling model MERCY v2.0 – linking atmospheric Hg to methyl mercury in fish
Reproducible and Relocatable Regional Ocean Modelling: Fundamentals and practices
Improved upper-ocean thermodynamical structure modeling with combined effects of surface waves and M2 internal tides on vertical mixing: a case study for the Indian Ocean
The bulk parameterizations of turbulent air–sea fluxes in NEMO4: the origin of sea surface temperature differences in a global model study
NeverWorld2: an idealized model hierarchy to investigate ocean mesoscale eddies across resolutions
Observing system simulation experiments reveal that subsurface temperature observations improve estimates of circulation and heat content in a dynamic western boundary current
Parallel implementation of the SHYFEM (System of HydrodYnamic Finite Element Modules) model
Block-structured, equal-workload, multi-grid-nesting interface for the Boussinesq wave model FUNWAVE-TVD (Total Variation Diminishing)
Evaluation of an emergent feature of sub-shelf melt oscillations from an idealized coupled ice sheet–ocean model using FISOC (v1.1) – ROMSIceShelf (v1.0) – Elmer/Ice (v9.0)
GNOM v1.0: an optimized steady-state model of the modern marine neodymium cycle
Implementation and evaluation of open boundary conditions for sea ice in a regional coupled ocean (ROMS) and sea ice (CICE) modeling system
ROMSPath v1.0: offline particle tracking for the Regional Ocean Modeling System (ROMS)
DINCAE 2.0: multivariate convolutional neural network with error estimates to reconstruct sea surface temperature satellite and altimetry observations
RADIv1: a non-steady-state early diagenetic model for ocean sediments in Julia and MATLAB/GNU Octave
IBI-CCS: a regional high-resolution model to simulate sea level in western Europe
Empirical Lagrangian parametrization for wind-driven mixing of buoyant particles at the ocean surface
Improvements in the regional South China Sea Operational Oceanography Forecasting System (SCSOFSv2)
Reconsideration of wind stress, wind waves, and turbulence in simulating wind-driven currents of shallow lakes in the Wave and Current Coupled Model (WCCM) version 1.0
ISWFoam: a numerical model for internal solitary wave simulation in continuously stratified fluids
PyCO2SYS v1.8: marine carbonate system calculations in Python
Plume spreading test case for coastal ocean models
The interpretation of temperature and salinity variables in numerical ocean model output and the calculation of heat fluxes and heat content
S2P3-R v2.0: computationally efficient modelling of shelf seas on regional to global scales
The Lagrangian-based Floating Macroalgal Growth and Drift Model (FMGDM v1.0): application to the Yellow Sea green tide
Nemo-Nordic 2.0: operational marine forecast model for the Baltic Sea
Australian tidal currents – assessment of a barotropic model (COMPAS v1.3.0 rev6631) with an unstructured grid
Sedapp v2021: a nonlinear diffusion-based forward stratigraphic model for shallow marine environments
A discrete interaction numerical model for coagulation and fragmentation of marine detritic particulate matter (Coagfrag v.1)
Parallel computing efficiency of SWAN 40.91
Integrating CVMix into GOTM (v6.0): a consistent framework for testing, comparing, and applying ocean mixing schemes
A NEMO-based model of Sargassum distribution in the tropical Atlantic: description of the model and sensitivity analysis (NEMO-Sarg1.0)
Evaluating the physical and biogeochemical state of the global ocean component of UKESM1 in CMIP6 historical simulations
Iron and sulfur cycling in the cGENIE.muffin Earth system model (v0.9.21)
BFM17 v1.0: a reduced biogeochemical flux model for upper-ocean biophysical simulations
A mechanistic analysis of tropical Pacific dynamic sea level in GFDL-OM4 under OMIP-I and OMIP-II forcings
Comparison of ocean vertical mixing schemes in the Max Planck Institute Earth System Model (MPI-ESM1.2)
Nairita Pal, Kristin N. Barton, Mark R. Petersen, Steven R. Brus, Darren Engwirda, Brian K. Arbic, Andrew F. Roberts, Joannes J. Westerink, and Damrongsak Wirasaet
Geosci. Model Dev., 16, 1297–1314, https://doi.org/10.5194/gmd-16-1297-2023, https://doi.org/10.5194/gmd-16-1297-2023, 2023
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Understanding tides is essential to accurately predict ocean currents. Over the next several decades coastal processes such as flooding and erosion will be severely impacted due to climate change. Tides affect currents along the coastal regions the most. In this paper we show the results of implementing tides in a global ocean model known as MPAS–Ocean. We also show how Antarctic ice shelf cavities affect global tides. Our work points towards future research with tide–ice interactions.
Sébastien Petton, Valérie Garnier, Matthieu Caillaud, Laurent Debreu, and Franck Dumas
Geosci. Model Dev., 16, 1191–1211, https://doi.org/10.5194/gmd-16-1191-2023, https://doi.org/10.5194/gmd-16-1191-2023, 2023
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The nesting AGRIF library is implemented in the MARS3D hydrodynamic model, a semi-implicit, free-surface numerical model which uses a time scheme as an alternating-direction implicit (ADI) algorithm. Two applications at the regional and coastal scale are introduced. We compare the two-nesting approach to the classic offline one-way approach, based on an in situ dataset. This method is an efficient means to significantly improve the physical hydrodynamics and unravel ecological challenges.
Noam S. Vogt-Vincent and Helen L. Johnson
Geosci. Model Dev., 16, 1163–1178, https://doi.org/10.5194/gmd-16-1163-2023, https://doi.org/10.5194/gmd-16-1163-2023, 2023
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Ocean currents transport things over large distances across the ocean surface. Predicting this transport is key for tackling many environmental problems, such as marine plastic pollution and coral reef resilience. However, doing this requires a good understanding ocean currents, which is currently lacking. Here, we present and validate state-of-the-art simulations for surface currents in the southwestern Indian Ocean, which will support future marine dispersal studies across this region.
Pengyang Song, Dmitry Sidorenko, Patrick Scholz, Maik Thomas, and Gerrit Lohmann
Geosci. Model Dev., 16, 383–405, https://doi.org/10.5194/gmd-16-383-2023, https://doi.org/10.5194/gmd-16-383-2023, 2023
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Tides have essential effects on the ocean and climate. Most previous research applies parameterised tidal mixing to discuss their effects in models. By comparing the effect of a tidal mixing parameterisation and tidal forcing on the ocean state, we assess the advantages and disadvantages of the two methods. Our results show that tidal mixing in the North Pacific Ocean strongly affects the global thermohaline circulation. We also list some effects that are not considered in the parameterisation.
Marko Rus, Anja Fettich, Matej Kristan, and Matjaž Ličer
Geosci. Model Dev., 16, 271–288, https://doi.org/10.5194/gmd-16-271-2023, https://doi.org/10.5194/gmd-16-271-2023, 2023
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We propose a new fast and reliable deep-learning architecture HIDRA2 for sea level and storm surge modeling. HIDRA2 features new feature encoders and a fusion-regression block. We test HIDRA2 on Adriatic storm surges, which depend on an interaction between tides and seiches. We demonstrate that HIDRA2 learns to effectively mimic the timing and amplitude of Adriatic seiches. This is essential for reliable HIDRA2 predictions of total storm surge sea levels.
Joao Marcos Azevedo Correia de Souza, Sutara H. Suanda, Phellipe P. Couto, Robert O. Smith, Colette Kerry, and Moninya Roughan
Geosci. Model Dev., 16, 211–231, https://doi.org/10.5194/gmd-16-211-2023, https://doi.org/10.5194/gmd-16-211-2023, 2023
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The current paper describes the configuration and evaluation of the Moana Ocean Hindcast, a > 25-year simulation of the ocean state around New Zealand using the Regional Ocean Modeling System v3.9. This is the first open-access, long-term, continuous, realistic ocean simulation for this region and provides information for improving the understanding of the ocean processes that affect the New Zealand exclusive economic zone.
Hao Huang, Pengyang Song, Shi Qiu, Jiaqi Guo, and Xueen Chen
Geosci. Model Dev., 16, 109–133, https://doi.org/10.5194/gmd-16-109-2023, https://doi.org/10.5194/gmd-16-109-2023, 2023
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The Oceanic Regional Circulation and Tide Model (ORCTM) is developed to reproduce internal solitary wave dynamics. The three-dimensional nonlinear momentum equations are involved with the nonhydrostatic pressure obtained via solving the Poisson equation. The validation experimental results agree with the internal wave theories and observations, demonstrating that the ORCTM can successfully describe the life cycle of nonlinear internal solitary waves under different oceanic environments.
David E. Gwyther, Shane R. Keating, Colette Kerry, and Moninya Roughan
Geosci. Model Dev., 16, 157–178, https://doi.org/10.5194/gmd-16-157-2023, https://doi.org/10.5194/gmd-16-157-2023, 2023
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Ocean eddies are important for weather, climate, biology, navigation, and search and rescue. Since eddies change rapidly, models that incorporate or assimilate observations are required to produce accurate eddy timings and locations, yet the model accuracy is rarely assessed below the surface. We use a unique type of ocean model experiment to assess three-dimensional eddy structure in the East Australian Current and explore two pathways in which this subsurface structure is being degraded.
Shun Ohishi, Takemasa Miyoshi, and Misako Kachi
Geosci. Model Dev., 15, 9057–9073, https://doi.org/10.5194/gmd-15-9057-2022, https://doi.org/10.5194/gmd-15-9057-2022, 2022
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An adaptive observation error inflation (AOEI) method was proposed for atmospheric data assimilation to mitigate erroneous analysis updates caused by large observation-minus-forecast differences for satellite brightness temperature around clear- and cloudy-sky boundaries. This study implemented the AOEI with an ocean data assimilation system, leading to an improvement of analysis accuracy and dynamical balance around the frontal regions with large meridional temperature differences.
Diego Bruciaferri, Marina Tonani, Isabella Ascione, Fahad Al Senafi, Enda O'Dea, Helene T. Hewitt, and Andrew Saulter
Geosci. Model Dev., 15, 8705–8730, https://doi.org/10.5194/gmd-15-8705-2022, https://doi.org/10.5194/gmd-15-8705-2022, 2022
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More accurate predictions of the Gulf's ocean dynamics are needed. We investigate the impact on the predictive skills of a numerical shelf sea model of the Gulf after changing a few key aspects. Increasing the lateral and vertical resolution and optimising the vertical coordinate system to best represent the leading physical processes at stake significantly improve the accuracy of the simulated dynamics. Additional work may be needed to get real benefit from using a more realistic bathymetry.
Matthias Gröger, Manja Placke, H. E. Markus Meier, Florian Börgel, Sandra-Esther Brunnabend, Cyril Dutheil, Ulf Gräwe, Magnus Hieronymus, Thomas Neumann, Hagen Radtke, Semjon Schimanke, Jian Su, and Germo Väli
Geosci. Model Dev., 15, 8613–8638, https://doi.org/10.5194/gmd-15-8613-2022, https://doi.org/10.5194/gmd-15-8613-2022, 2022
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Comparisons of oceanographic climate data from different models often suffer from different model setups, forcing fields, and output of variables. This paper provides a protocol to harmonize these elements to set up multidecadal simulations for the Baltic Sea, a marginal sea in Europe. First results are shown from six different model simulations from four different model platforms. Topical studies for upwelling, marine heat waves, and stratification are also assessed.
Shun Ohishi, Tsutomu Hihara, Hidenori Aiki, Joji Ishizaka, Yasumasa Miyazawa, Misako Kachi, and Takemasa Miyoshi
Geosci. Model Dev., 15, 8395–8410, https://doi.org/10.5194/gmd-15-8395-2022, https://doi.org/10.5194/gmd-15-8395-2022, 2022
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We develop an ensemble-Kalman-filter-based regional ocean data assimilation system in which satellite and in situ observations are assimilated at a daily frequency. We find the best setting for dynamical balance and accuracy based on sensitivity experiments focused on how to inflate the ensemble spread and how to apply the analysis update to the model evolution. This study has a broader impact on more general data assimilation systems in which the initial shocks are a significant issue.
Hector S. Torres, Patrice Klein, Jinbo Wang, Alexander Wineteer, Bo Qiu, Andrew F. Thompson, Lionel Renault, Ernesto Rodriguez, Dimitris Menemenlis, Andrea Molod, Christopher N. Hill, Ehud Strobach, Hong Zhang, Mar Flexas, and Dragana Perkovic-Martin
Geosci. Model Dev., 15, 8041–8058, https://doi.org/10.5194/gmd-15-8041-2022, https://doi.org/10.5194/gmd-15-8041-2022, 2022
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Wind work at the air-sea interface is the scalar product of winds and currents and is the transfer of kinetic energy between the ocean and the atmosphere. Using a new global coupled ocean-atmosphere simulation performed at kilometer resolution, we show that all scales of winds and currents impact the ocean dynamics at spatial and temporal scales. The consequential interplay of surface winds and currents in the numerical simulation motivates the need for a winds and currents satellite mission.
Bin Xiao, Fangli Qiao, Qi Shu, Xunqiang Yin, Guansuo Wang, and Shihong Wang
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-254, https://doi.org/10.5194/gmd-2022-254, 2022
Revised manuscript accepted for GMD
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A new global surface wave-tide-circulation coupled ocean model FIO-COM32 with resolution of 1/32° × 1/32° is developed and validated. Both the promotion of the horizontal resolution and included physical processes are proved to be important contributors to the significant improvements of FIO-COM32 simulations. It should be the time to merge these separated model components (surface wave, tidal current and ocean circulation) for new generation ocean model development.
Johannes Bieser, David Amptmeijer, Ute Daewel, Joachim Kuss, Anne L. Soerensen, and Corinna Schrum
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2021-427, https://doi.org/10.5194/gmd-2021-427, 2022
Revised manuscript accepted for GMD
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We developed a 3d model for mercury (Hg) cycling and bioaccumulation in the ocean. Hg is a major global pollutant regulated under the UN Minamata Convention. Anthropogenic Hg emission are transported globally and eventually reach the worlds Oceans. There, Hg is transformed into an even more toxic and bioaccumulative pollutant: Methylmercury (MeHg). The MERCY model is able to predict the fate of Hg in the ocean, the formation of MeHg, and its accumulation in the food web.
Jeff A. Polton, James Harle, Jason Holt, Anna Katavouta, Dale Partridge, Jenny Jardine, Sarah Wakelin, Julia Rulent, Anthony Wise, Katherine Hutchinson, David Byrne, Diego Bruciaferri, Enda O'Dea, Michela De Dominicis, Pierre Mathiot, Andrew Coward, Andrew Yool, Julien Palmieri, Gennadi Lessin, Gabriela Mayorga-Adame, Valerie Le Guennec, Alex Arnold, and Clement Rousset
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-217, https://doi.org/10.5194/gmd-2022-217, 2022
Revised manuscript accepted for GMD
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The aim is to increase the capacity of the modelling community to respond to societally important questions that require ocean modelling. The concept of Reproducibility for regional ocean modelling is developed: advocating methods for reproducible workflows and standardised methods of assessment. Then, targeting the NEMO framework, we give practical advice and worked examples; highlighting key considerations that will expedite development cycle and up skill the community user community.
Zhanpeng Zhuang, Quanan Zheng, Yongzeng Yang, Zhenya Song, Yeli Yuan, Chaojie Zhou, Xinhua Zhao, Ting Zhang, and Jing Xie
Geosci. Model Dev., 15, 7221–7241, https://doi.org/10.5194/gmd-15-7221-2022, https://doi.org/10.5194/gmd-15-7221-2022, 2022
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We evaluate the impacts of surface waves and internal tides on the upper-ocean mixing in the Indian Ocean. The surface-wave-generated turbulent mixing is dominant if depth is < 30 m, while the internal-tide-induced mixing is larger than surface waves in the ocean interior from 40
to 130 m. The simulated thermal structure, mixed layer depth and surface current are all improved when the mixing schemes are jointly incorporated into the ocean model because of the strengthened vertical mixing.
Giulia Bonino, Doroteaciro Iovino, Laurent Brodeau, and Simona Masina
Geosci. Model Dev., 15, 6873–6889, https://doi.org/10.5194/gmd-15-6873-2022, https://doi.org/10.5194/gmd-15-6873-2022, 2022
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The sea surface temperature (SST) is highly influenced by the transfer of energy driven by turbulent air–sea fluxes (TASFs). In the NEMO ocean general circulation model, TASFs are computed by means of bulk formulas. Bulk formulas require the choice of a given bulk parameterization, which influences the magnitudes of the TASFs. Our results show that parameterization-related SST differences are primarily sensitive to the wind stress differences across parameterizations.
Gustavo M. Marques, Nora Loose, Elizabeth Yankovsky, Jacob M. Steinberg, Chiung-Yin Chang, Neeraja Bhamidipati, Alistair Adcroft, Baylor Fox-Kemper, Stephen M. Griffies, Robert W. Hallberg, Malte F. Jansen, Hemant Khatri, and Laure Zanna
Geosci. Model Dev., 15, 6567–6579, https://doi.org/10.5194/gmd-15-6567-2022, https://doi.org/10.5194/gmd-15-6567-2022, 2022
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We present an idealized ocean model configuration and a set of simulations performed using varying horizontal grid spacing. While the model domain is idealized, it resembles important geometric features of the Atlantic and Southern oceans. The simulations described here serve as a framework to effectively study mesoscale eddy dynamics, to investigate the effect of mesoscale eddies on the large-scale dynamics, and to test and evaluate eddy parameterizations.
David E. Gwyther, Colette Kerry, Moninya Roughan, and Shane R. Keating
Geosci. Model Dev., 15, 6541–6565, https://doi.org/10.5194/gmd-15-6541-2022, https://doi.org/10.5194/gmd-15-6541-2022, 2022
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The ocean current flowing along the southeastern coast of Australia is called the East Australian Current (EAC). Using computer simulations, we tested how surface and subsurface observations might improve models of the EAC. Subsurface observations are particularly important for improving simulations, and if made in the correct location and time, can have impact 600 km upstream. The stability of the current affects model estimates could be capitalized upon in future observing strategies.
Giorgio Micaletto, Ivano Barletta, Silvia Mocavero, Ivan Federico, Italo Epicoco, Giorgia Verri, Giovanni Coppini, Pasquale Schiano, Giovanni Aloisio, and Nadia Pinardi
Geosci. Model Dev., 15, 6025–6046, https://doi.org/10.5194/gmd-15-6025-2022, https://doi.org/10.5194/gmd-15-6025-2022, 2022
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The full exploitation of supercomputing architectures requires a deep revision of the current climate models. This paper presents the parallelization of the three-dimensional hydrodynamic model SHYFEM (System of HydrodYnamic Finite Element Modules). Optimized numerical libraries were used to partition the model domain and solve the sparse linear system of equations in parallel. The performance assessment demonstrates a good level of scalability with a realistic configuration used as a benchmark.
Young-Kwang Choi, Fengyan Shi, Matt Malej, Jane M. Smith, James T. Kirby, and Stephan T. Grilli
Geosci. Model Dev., 15, 5441–5459, https://doi.org/10.5194/gmd-15-5441-2022, https://doi.org/10.5194/gmd-15-5441-2022, 2022
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The multi-grid-nesting technique is an important methodology used for modeling transoceanic tsunamis and coastal effects. In this study, we developed a two-way nesting interface in a multi-grid-nesting system for the Boussinesq wave model FUNWAVE-TVD. The interface acts as a
backboneof the nesting framework, handling data input, output, time sequencing, and internal interactions between grids at different scales.
Chen Zhao, Rupert Gladstone, Benjamin Keith Galton-Fenzi, David Gwyther, and Tore Hattermann
Geosci. Model Dev., 15, 5421–5439, https://doi.org/10.5194/gmd-15-5421-2022, https://doi.org/10.5194/gmd-15-5421-2022, 2022
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We use a coupled ice–ocean model to explore an oscillation feature found in several contributing models to MISOMIP1. The oscillation is closely related to the discretized grounding line retreat and likely strengthened by the buoyancy–melt feedback and/or melt–geometry feedback near the grounding line, and frequent ice–ocean coupling. Our model choices have a non-trivial impact on mean melt and ocean circulation strength, which might be interesting for the coupled ice–ocean community.
Benoît Pasquier, Sophia K. V. Hines, Hengdi Liang, Yingzhe Wu, Steven L. Goldstein, and Seth G. John
Geosci. Model Dev., 15, 4625–4656, https://doi.org/10.5194/gmd-15-4625-2022, https://doi.org/10.5194/gmd-15-4625-2022, 2022
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Neodymium isotopes in seawater have the potential to provide key information about ocean circulation, both today and in the past. This can shed light on the underlying drivers of global climate, which will improve our ability to predict future climate change, but uncertainties in our understanding of neodymium cycling have limited use of this tracer. We present a new model of neodymium in the modern ocean that runs extremely fast, matches observations, and is freely available for development.
Pedro Duarte, Jostein Brændshøi, Dmitry Shcherbin, Pauline Barras, Jon Albretsen, Yvonne Gusdal, Nicholas Szapiro, Andreas Martinsen, Annette Samuelsen, Keguang Wang, and Jens Boldingh Debernard
Geosci. Model Dev., 15, 4373–4392, https://doi.org/10.5194/gmd-15-4373-2022, https://doi.org/10.5194/gmd-15-4373-2022, 2022
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Sea ice models are often implemented for very large domains beyond the regions of sea ice formation, such as the whole Arctic or all of Antarctica. In this study, we implement changes in the Los Alamos Sea Ice Model, allowing it to be implemented for relatively small regions within the Arctic or Antarctica and yet considering the presence and influence of sea ice outside the represented areas. Such regional implementations are important when spatially detailed results are required.
Elias J. Hunter, Heidi L. Fuchs, John L. Wilkin, Gregory P. Gerbi, Robert J. Chant, and Jessica C. Garwood
Geosci. Model Dev., 15, 4297–4311, https://doi.org/10.5194/gmd-15-4297-2022, https://doi.org/10.5194/gmd-15-4297-2022, 2022
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ROMSPath is an offline particle tracking model tailored for use with output from Regional Ocean Modeling System (ROMS) simulations. It is an update to an established system, the Lagrangian TRANSport (LTRANS) model, including a number of improvements. These include a modification of the model coordinate system which improved accuracy and numerical efficiency, and added functionality for nested grids and Stokes drift.
Alexander Barth, Aida Alvera-Azcárate, Charles Troupin, and Jean-Marie Beckers
Geosci. Model Dev., 15, 2183–2196, https://doi.org/10.5194/gmd-15-2183-2022, https://doi.org/10.5194/gmd-15-2183-2022, 2022
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Earth-observing satellites provide routine measurement of several ocean parameters. However, these datasets have a significant amount of missing data due to the presence of clouds or other limitations of the employed sensors. This paper describes a method to infer the value of the missing satellite data based on a convolutional autoencoder (a specific type of neural network architecture). The technique also provides a reliable error estimate of the interpolated value.
Olivier Sulpis, Matthew P. Humphreys, Monica M. Wilhelmus, Dustin Carroll, William M. Berelson, Dimitris Menemenlis, Jack J. Middelburg, and Jess F. Adkins
Geosci. Model Dev., 15, 2105–2131, https://doi.org/10.5194/gmd-15-2105-2022, https://doi.org/10.5194/gmd-15-2105-2022, 2022
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A quarter of the surface of the Earth is covered by marine sediments rich in calcium carbonates, and their dissolution acts as a giant antacid tablet protecting the ocean against human-made acidification caused by massive CO2 emissions. Here, we present a new model of sediment chemistry that incorporates the latest experimental findings on calcium carbonate dissolution kinetics. This model can be used to predict how marine sediments evolve through time in response to environmental perturbations.
Alisée A. Chaigneau, Guillaume Reffray, Aurore Voldoire, and Angélique Melet
Geosci. Model Dev., 15, 2035–2062, https://doi.org/10.5194/gmd-15-2035-2022, https://doi.org/10.5194/gmd-15-2035-2022, 2022
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Climate-change-induced sea level rise is a major threat for coastal and low-lying regions. Projections of coastal sea level changes are thus of great interest for coastal risk assessment and have significantly developed in recent years. In this paper, the objective is to provide high-resolution (6 km) projections of sea level changes in the northeastern Atlantic region bordering western Europe. For that purpose, a regional model is used to refine existing coarse global projections.
Victor Onink, Erik van Sebille, and Charlotte Laufkötter
Geosci. Model Dev., 15, 1995–2012, https://doi.org/10.5194/gmd-15-1995-2022, https://doi.org/10.5194/gmd-15-1995-2022, 2022
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Turbulent mixing is a vital process in 3D modeling of particle transport in the ocean. However, since turbulence occurs on very short spatial scales and timescales, large-scale ocean models generally have highly simplified turbulence representations. We have developed parametrizations for the vertical turbulent transport of buoyant particles that can be easily applied in a large-scale particle tracking model. The predicted vertical concentration profiles match microplastic observations well.
Xueming Zhu, Ziqing Zu, Shihe Ren, Miaoyin Zhang, Yunfei Zhang, Hui Wang, and Ang Li
Geosci. Model Dev., 15, 995–1015, https://doi.org/10.5194/gmd-15-995-2022, https://doi.org/10.5194/gmd-15-995-2022, 2022
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SCSOFS has provided daily updated marine forecasting in the South China Sea for the next 5 d since 2013. Comprehensive updates have been conducted to the configurations of SCSOFS's physical model and data assimilation scheme in order to improve its forecasting skill. The three most sensitive updates are highlighted. Scientific comparison and accuracy assessment results indicate that remarkable improvements have been achieved in SCSOFSv2 with respect to the original version SCSOFSv1.
Tingfeng Wu, Boqiang Qin, Anning Huang, Yongwei Sheng, Shunxin Feng, and Céline Casenave
Geosci. Model Dev., 15, 745–769, https://doi.org/10.5194/gmd-15-745-2022, https://doi.org/10.5194/gmd-15-745-2022, 2022
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Most hydrodynamic models were initially developed based in marine environments. They cannot be directly applied to large lakes. Based on field observations and numerical experiments of a large shallow lake, we developed a hydrodynamic model by adopting new schemes of wind stress, wind waves, and turbulence for large lakes. Our model can greatly improve the simulation of lake currents. This study will be a reminder to limnologists to prudently use ocean models to study lake hydrodynamics.
Jingyuan Li, Qinghe Zhang, and Tongqing Chen
Geosci. Model Dev., 15, 105–127, https://doi.org/10.5194/gmd-15-105-2022, https://doi.org/10.5194/gmd-15-105-2022, 2022
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A numerical model, ISWFoam with a modified k–ω SST model, is developed to simulate internal solitary waves (ISWs) in continuously stratified, incompressible, viscous fluids based on a fully three-dimensional (3D) Navier–Stokes equation with the finite-volume method. ISWFoam can accurately simulate the generation and evolution of ISWs, the ISW breaking phenomenon, waveform inversion of ISWs, and the interaction between ISWs and complex topography.
Matthew P. Humphreys, Ernie R. Lewis, Jonathan D. Sharp, and Denis Pierrot
Geosci. Model Dev., 15, 15–43, https://doi.org/10.5194/gmd-15-15-2022, https://doi.org/10.5194/gmd-15-15-2022, 2022
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The ocean helps to mitigate our impact on Earth's climate by absorbing about a quarter of the carbon dioxide (CO2) released by human activities each year. However, once absorbed, chemical reactions between CO2 and water reduce seawater pH (
ocean acidification), which may have adverse effects on marine ecosystems. Our Python package, PyCO2SYS, models the chemical reactions of CO2 in seawater, allowing us to quantify the corresponding changes in pH and related chemical properties.
Vera Fofonova, Tuomas Kärnä, Knut Klingbeil, Alexey Androsov, Ivan Kuznetsov, Dmitry Sidorenko, Sergey Danilov, Hans Burchard, and Karen Helen Wiltshire
Geosci. Model Dev., 14, 6945–6975, https://doi.org/10.5194/gmd-14-6945-2021, https://doi.org/10.5194/gmd-14-6945-2021, 2021
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We present a test case of river plume spreading to evaluate coastal ocean models. Our test case reveals the level of numerical mixing (due to parameterizations used and numerical treatment of processes in the model) and the ability of models to reproduce complex dynamics. The major result of our comparative study is that accuracy in reproducing the analytical solution depends less on the type of applied model architecture or numerical grid than it does on the type of advection scheme.
Trevor J. McDougall, Paul M. Barker, Ryan M. Holmes, Rich Pawlowicz, Stephen M. Griffies, and Paul J. Durack
Geosci. Model Dev., 14, 6445–6466, https://doi.org/10.5194/gmd-14-6445-2021, https://doi.org/10.5194/gmd-14-6445-2021, 2021
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We show that the way that the air–sea heat flux is treated in ocean models means that the model's temperature variable should be interpreted as being Conservative Temperature, irrespective of whether the equation of state used in an ocean model is EOS-80 or TEOS-10.
Paul R. Halloran, Jennifer K. McWhorter, Beatriz Arellano Nava, Robert Marsh, and William Skirving
Geosci. Model Dev., 14, 6177–6195, https://doi.org/10.5194/gmd-14-6177-2021, https://doi.org/10.5194/gmd-14-6177-2021, 2021
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This paper describes the latest version of a simple model for simulating coastal oceanography in response to changes in weather and climate. The latest revision of this model makes scientific improvements but focuses on improvements that allow the model to be run simply at large scales and for long periods of time to explore the implications of (for example) future climate change along large areas of coastline.
Fucang Zhou, Jianzhong Ge, Dongyan Liu, Pingxing Ding, Changsheng Chen, and Xiaodao Wei
Geosci. Model Dev., 14, 6049–6070, https://doi.org/10.5194/gmd-14-6049-2021, https://doi.org/10.5194/gmd-14-6049-2021, 2021
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In this study, a physical–ecological model, the Floating Macroalgal Growth and Drift Model (FMGDM), was developed to determine the dynamic growth and drifting pattern of floating macroalgae. Based on Lagrangian tracking, the macroalgae bloom is jointly controlled by ocean flows, sea surface wind, temperature, irradiation, and nutrients. The FMGDM was robust in successfully reproducing the spatial and temporal dynamics of the massive green tide around the Yellow Sea.
Tuomas Kärnä, Patrik Ljungemyr, Saeed Falahat, Ida Ringgaard, Lars Axell, Vasily Korabel, Jens Murawski, Ilja Maljutenko, Anja Lindenthal, Simon Jandt-Scheelke, Svetlana Verjovkina, Ina Lorkowski, Priidik Lagemaa, Jun She, Laura Tuomi, Adam Nord, and Vibeke Huess
Geosci. Model Dev., 14, 5731–5749, https://doi.org/10.5194/gmd-14-5731-2021, https://doi.org/10.5194/gmd-14-5731-2021, 2021
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We present Nemo-Nordic 2.0, a novel operational marine model for the Baltic Sea. The model covers the Baltic Sea and the North Sea with approximately 1 nmi resolution. We validate the model's performance against sea level, water temperature, and salinity observations, as well as sea ice charts. The skill analysis demonstrates that Nemo-Nordic 2.0 can reproduce the hydrographic features of the Baltic Sea.
David A. Griffin, Mike Herzfeld, Mark Hemer, and Darren Engwirda
Geosci. Model Dev., 14, 5561–5582, https://doi.org/10.5194/gmd-14-5561-2021, https://doi.org/10.5194/gmd-14-5561-2021, 2021
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In support of the developing ocean renewable energy sector, and indeed all mariners, we have developed a new tidal model for Australian waters and thoroughly evaluated it using a new compilation of tide gauge and current meter data. We show that while there is certainly room for improvement, the model provides useful predictions of tidal currents for about 80 % (by area) of Australian shelf waters. So we intend to commence publishing tidal current predictions for those regions soon.
Jingzhe Li, Piyang Liu, Shuyu Sun, Zhifeng Sun, Yongzhang Zhou, Liang Gong, Jinliang Zhang, and Dongxing Du
Geosci. Model Dev., 14, 4925–4937, https://doi.org/10.5194/gmd-14-4925-2021, https://doi.org/10.5194/gmd-14-4925-2021, 2021
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This paper introduces Sedapp, a basin fill simulation tool. Sedapp is an open-source computer code written in R language. Using this program, one can simulate the formation of sedimentary strata, especially in shallow marine environments injected by rivers. With proper parameter settings, the simulation results are very similar to the real geological bodies. Sedapp can also be used in continental fault basin environments, which may serve as a tool for oil exploration.
Gwenaëlle Gremion, Louis-Philippe Nadeau, Christiane Dufresne, Irene R. Schloss, Philippe Archambault, and Dany Dumont
Geosci. Model Dev., 14, 4535–4554, https://doi.org/10.5194/gmd-14-4535-2021, https://doi.org/10.5194/gmd-14-4535-2021, 2021
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An accurate description of detritic organic particles is key to improving estimations of carbon export into the ocean abyss in ocean general circulation models. Yet, most parametrization are numerically impractical due to the required number of tracers needed to resolve the particle size spectrum. Here, a new parametrization that aims to minimize the tracers number while accurately describing the particles dynamics is developed and tested in a series of idealized numerical experiments.
Christo Rautenbach, Julia C. Mullarney, and Karin R. Bryan
Geosci. Model Dev., 14, 4241–4247, https://doi.org/10.5194/gmd-14-4241-2021, https://doi.org/10.5194/gmd-14-4241-2021, 2021
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The simulation of ocean waves is important for various reasons, e.g. ship route safety and coastal vulnerability assessments. SWAN is a popular tool with which ocean waves may be predicted. Simulations using this tool can be computationally expensive. The present study thus aimed to understand which typical parallel-computing SWAN model set-up will be most effective. There thus do exist configurations where these simulations are most time-saving and effective.
Qing Li, Jorn Bruggeman, Hans Burchard, Knut Klingbeil, Lars Umlauf, and Karsten Bolding
Geosci. Model Dev., 14, 4261–4282, https://doi.org/10.5194/gmd-14-4261-2021, https://doi.org/10.5194/gmd-14-4261-2021, 2021
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Different ocean vertical mixing schemes are usually developed in different modeling framework, making the comparison across such schemes difficult. Here, we develop a consistent framework for testing, comparing, and applying different ocean mixing schemes by integrating CVMix into GOTM, which also extends the capability of GOTM towards including the effects of ocean surface waves. A suite of test cases and toolsets for developing and evaluating ocean mixing schemes is also described.
Julien Jouanno, Rachid Benshila, Léo Berline, Antonin Soulié, Marie-Hélène Radenac, Guillaume Morvan, Frédéric Diaz, Julio Sheinbaum, Cristele Chevalier, Thierry Thibaut, Thomas Changeux, Frédéric Menard, Sarah Berthet, Olivier Aumont, Christian Ethé, Pierre Nabat, and Marc Mallet
Geosci. Model Dev., 14, 4069–4086, https://doi.org/10.5194/gmd-14-4069-2021, https://doi.org/10.5194/gmd-14-4069-2021, 2021
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The tropical Atlantic has been facing a massive proliferation of Sargassum since 2011, with severe environmental and socioeconomic impacts. We developed a modeling framework based on the NEMO ocean model, which integrates transport by currents and waves, and physiology of Sargassum with varying internal nutrient quota, and considers stranding at the coast. Results demonstrate the ability of the model to reproduce and forecast the seasonal cycle and large-scale distribution of Sargassum biomass.
Andrew Yool, Julien Palmiéri, Colin G. Jones, Lee de Mora, Till Kuhlbrodt, Ekatarina E. Popova, A. J. George Nurser, Joel Hirschi, Adam T. Blaker, Andrew C. Coward, Edward W. Blockley, and Alistair A. Sellar
Geosci. Model Dev., 14, 3437–3472, https://doi.org/10.5194/gmd-14-3437-2021, https://doi.org/10.5194/gmd-14-3437-2021, 2021
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The ocean plays a key role in modulating the Earth’s climate. Understanding this role is critical when using models to project future climate change. Consequently, it is necessary to evaluate their realism against the ocean's observed state. Here we validate UKESM1, a new Earth system model, focusing on the realism of its ocean physics and circulation, as well as its biological cycles and productivity. While we identify biases, generally the model performs well over a wide range of properties.
Sebastiaan J. van de Velde, Dominik Hülse, Christopher T. Reinhard, and Andy Ridgwell
Geosci. Model Dev., 14, 2713–2745, https://doi.org/10.5194/gmd-14-2713-2021, https://doi.org/10.5194/gmd-14-2713-2021, 2021
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Biogeochemical interactions between iron and sulfur are central to the long-term biogeochemical evolution of Earth’s oceans. Here, we introduce an iron–sulphur cycle in a model of Earth's oceans. Our analyses show that the results of the model are robust towards parameter choices and that simulated concentrations and reactions are comparable to those observed in ancient ocean analogues (anoxic lakes). Our model represents an important step forward in the study of iron–sulfur cycling.
Katherine M. Smith, Skyler Kern, Peter E. Hamlington, Marco Zavatarelli, Nadia Pinardi, Emily F. Klee, and Kyle E. Niemeyer
Geosci. Model Dev., 14, 2419–2442, https://doi.org/10.5194/gmd-14-2419-2021, https://doi.org/10.5194/gmd-14-2419-2021, 2021
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We present a newly developed reduced-order biogeochemical flux model that is complex and flexible enough to capture open-ocean ecosystem dynamics but reduced enough to incorporate into highly resolved numerical simulations with limited additional computational cost. The model provides improved correlations between model output and field data, indicating that significant improvements in the reproduction of real-world data can be achieved with a small number of variables.
Chia-Wei Hsu, Jianjun Yin, Stephen M. Griffies, and Raphael Dussin
Geosci. Model Dev., 14, 2471–2502, https://doi.org/10.5194/gmd-14-2471-2021, https://doi.org/10.5194/gmd-14-2471-2021, 2021
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The new surface forcing from JRA55-do (OMIP II) significantly improved the underestimated sea level trend across the entire Pacific Ocean along 10° N in the simulation forced by CORE (OMIP I). We summarize and list out the reasons for the existing sea level biases across all studied timescales as a reference for improving the sea level simulation in the future. This study on the evaluation and improvement of ocean climate models should be of broad interest to a large modeling community.
Oliver Gutjahr, Nils Brüggemann, Helmuth Haak, Johann H. Jungclaus, Dian A. Putrasahan, Katja Lohmann, and Jin-Song von Storch
Geosci. Model Dev., 14, 2317–2349, https://doi.org/10.5194/gmd-14-2317-2021, https://doi.org/10.5194/gmd-14-2317-2021, 2021
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We compare four ocean vertical mixing schemes in 100-year coupled simulations with the Max Planck Institute Earth System Model (MPI-ESM1.2) and analyse their model biases. Overall, the mixing schemes modify biases in the ocean interior that vary with region and variable but produce a similar global bias pattern. We therefore cannot classify any scheme as superior but conclude that the chosen mixing scheme may be important for regional biases.
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Short summary
To be efficient on supercomputers, software must be high-performance at computing many concurrent tasks. Communications between tasks is often necessary but time consuming, and ocean modelling software NEMO 4.0 is no exception.
In this work we describe approaches enabling fewer communications, an optimization to share the workload more equally between tasks and a new flexible configuration to assess NEMO's performance easily.
To be efficient on supercomputers, software must be high-performance at computing many...
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