COUPLED BISTABLE MAPS: A TOOL TO STUDY CONVECTION PARAMETERIZATION IN OCEAN MODELS

We present a study of ocean convection parameterization based on a novel approach which includes both eddy diffusion and advection and consists of a two-dimensional lattice of bistable maps. This approach retains important features of usual grid models and allows to assess the relative roles of diffusion and advection in the spreading of convective cells. For large diffusion our model exhibits a phase transition from convective patterns to a homogeneous state over the entire lattice. In hysteresis experiments we find staircase behavior depending on stability thresholds of local convection patterns. This nonphysical behavior is suspected to induce spurious abrupt changes in the spreading of convection in ocean models. The final steady state of convective cells depends not only on the magnitude of the advective velocity but also on its direction, implying a possible bias in the development of convective patterns. Such bias points to the need for an appropriate choice of grid geometry in ocean modeling.

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Mixing Inferred from an Ocean Climatology and Surface Fluxes

Journal of Physical Oceanography ◽

10.1175/jpo-d-16-0125.1 ◽

2017 ◽

Vol 47 (3) ◽

pp. 667-687 ◽

Cited By ~ 18

Author(s):

Sjoerd Groeskamp ◽

Bernadette M. Sloyan ◽

Jan D. Zika ◽

Trevor J. McDougall

Keyword(s):

Ocean Circulation ◽

Climate Models ◽

Eddy Diffusion ◽

Surface Fluxes ◽

Small Scale ◽

Vertical Variation ◽

Mixing Coefficient ◽

Order Of Magnitude ◽

Ocean Models ◽

Isopycnal Mixing

AbstractThis study provides observation-based estimates, determined by inverse methods, of horizontal and isopycnal eddy diffusion coefficients KH and KI, respectively, the small-scale mixing coefficient D, and the diathermohaline streamfunction Ψ. The inverse solution of Ψ represents the ocean circulation in Absolute Salinity SA and Conservative Temperature Θ coordinates. The authors suggest that the observation-based estimate of Ψ will be useful for comparison with equivalent diagnostics from numerical climate models. The estimates of KH and KI represent horizontal eddy mixing in the mixed layer and isopycnal eddy mixing in the ocean interior, respectively. This study finds that the solution for D and KH are comparable to existing estimates. The solution for KI is one of the first observation-based global and full-depth constrained estimates of isopycnal mixing and indicates that KI is an order of magnitude smaller than KH. This suggests that there is a large vertical variation in the eddy mixing coefficient, which is generally not included in ocean models. With ocean models being very sensitive to the choice of isopycnal mixing, this result suggests that further investigation of the spatial structure of isopycnal eddy mixing from observations is required.

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A method for applying lateral surface eddy diffusion in ocean models with a general vertical coordinate

10.1002/essoar.10506862.1 ◽

2021 ◽

Author(s):

Gustavo M. Marques ◽

Andrew E. Shao ◽

Scott D. Bachman ◽

Gokhan Danabasoglu ◽

Frank O. Bryan

Keyword(s):

Lateral Surface ◽

Eddy Diffusion ◽

Vertical Coordinate ◽

Ocean Models

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OpenArray v1.0: a simple operator library for the decoupling of ocean modeling and parallel computing

Geoscientific Model Development ◽

10.5194/gmd-12-4729-2019 ◽

2019 ◽

Vol 12 (11) ◽

pp. 4729-4749

Author(s):

Xiaomeng Huang ◽

Xing Huang ◽

Dong Wang ◽

Qi Wu ◽

Yi Li ◽

...

Keyword(s):

Parallel Computing ◽

Climate Modeling ◽

Ocean Model ◽

Ocean Modeling ◽

Computational Techniques ◽

Promising Alternative ◽

Parallel Efficiency ◽

Strong Scaling ◽

Ocean Models ◽

Simple Operator

Abstract. Rapidly evolving computational techniques are making a large gap between scientific aspiration and code implementation in climate modeling. In this work, we design a simple computing library to bridge the gap and decouple the work of ocean modeling from parallel computing. This library provides 12 basic operators that feature user-friendly interfaces, effective programming, and implicit parallelism. Several state-of-the-art computing techniques, including computing graph and just-in-time compiling, are employed to parallelize the seemingly serial code and speed up the ocean models. These operator interfaces are designed using native Fortran programming language to smooth the learning curve. We further implement a highly readable and efficient ocean model that contains only 1860 lines of code but achieves a 91 % parallel efficiency in strong scaling and 99 % parallel efficiency in weak scaling with 4096 Intel CPU cores. This ocean model also exhibits excellent scalability on the heterogeneous Sunway TaihuLight supercomputer. This work presents a promising alternative tool for the development of ocean models.

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On the use of Schwarz–Christoffel conformal mappings to the grid generation for global ocean models

Geoscientific Model Development Discussions ◽

10.5194/gmdd-8-1337-2015 ◽

2015 ◽

Vol 8 (2) ◽

pp. 1337-1373

Author(s):

S. Xu ◽

B. Wang ◽

J. Liu

Keyword(s):

Conformal Mapping ◽

General Circulation ◽

Grid Generation ◽

General Circulation Models ◽

Ocean Modeling ◽

Global Ocean ◽

Generation Task ◽

Grid Design ◽

Ocean Models ◽

New Algorithms

Abstract. In this article we propose two conformal mapping based grid generation algorithms for global ocean general circulation models (OGCMs). Contrary to conventional, analytical forms based dipolar or tripolar grids, the new algorithms are based on Schwarz–Christoffel (SC) conformal mapping with prescribed boundary information. While dealing with the basic grid design problem of pole relocation, these new algorithms also address more advanced issues such as smoothed scaling factor, or the new requirements on OGCM grids arisen from the recent trend of high-resolution and multi-scale modeling. The proposed grid generation algorithm could potentially achieve the alignment of grid lines to coastlines, enhanced spatial resolution in coastal regions, and easier computational load balance. Since the generated grids are still orthogonal curvilinear, they can be readily utilized in existing Bryan–Cox–Semtner type ocean models. The proposed methodology can also be applied to the grid generation task for regional ocean modeling where complex land–ocean distribution is present.

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A novel approach to assess the hydrodynamic effects of a salmon farm in a Patagonian channel: Coupling between regional ocean modeling and high resolution les simulation

Aquaculture ◽

10.1016/j.aquaculture.2018.05.003 ◽

2018 ◽

Vol 495 ◽

pp. 115-129 ◽

Cited By ~ 3

Author(s):

Julio Herrera ◽

Pablo Cornejo ◽

Héctor Hito Sepúlveda ◽

Osvaldo Artal ◽

Renato A. Quiñones

Keyword(s):

High Resolution ◽

Ocean Modeling ◽

Channel Coupling ◽

Salmon Farm ◽

Novel Approach ◽

Hydrodynamic Effects

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How to use mixed precision in ocean models: exploring a potential reduction of numerical precision in NEMO 4.0 and ROMS 3.6

Geoscientific Model Development ◽

10.5194/gmd-12-3135-2019 ◽

2019 ◽

Vol 12 (7) ◽

pp. 3135-3148 ◽

Cited By ~ 3

Author(s):

Oriol Tintó Prims ◽

Mario C. Acosta ◽

Andrew M. Moore ◽

Miguel Castrillo ◽

Kim Serradell ◽

...

Keyword(s):

Real Variable ◽

Ocean Modeling ◽

Divide And Conquer ◽

Regional Ocean Modeling System ◽

Divide And Conquer Algorithm ◽

Complex Interactions ◽

Computational Performance ◽

Mixed Precision ◽

Ocean Models ◽

Numerical Precision

Abstract. Mixed-precision approaches can provide substantial speed-ups for both computing- and memory-bound codes with little effort. Most scientific codes have overengineered the numerical precision, leading to a situation in which models are using more resources than required without knowing where they are required and where they are not. Consequently, it is possible to improve computational performance by establishing a more appropriate choice of precision. The only input that is needed is a method to determine which real variables can be represented with fewer bits without affecting the accuracy of the results. This paper presents a novel method that enables modern and legacy codes to benefit from a reduction of the precision of certain variables without sacrificing accuracy. It consists of a simple idea: we reduce the precision of a group of variables and measure how it affects the outputs. Then we can evaluate the level of precision that they truly need. Modifying and recompiling the code for each case that has to be evaluated would require a prohibitive amount of effort. Instead, the method presented in this paper relies on the use of a tool called a reduced-precision emulator (RPE) that can significantly streamline the process. Using the RPE and a list of parameters containing the precisions that will be used for each real variable in the code, it is possible within a single binary to emulate the effect on the outputs of a specific choice of precision. When we are able to emulate the effects of reduced precision, we can proceed with the design of the tests that will give us knowledge of the sensitivity of the model variables regarding their numerical precision. The number of possible combinations is prohibitively large and therefore impossible to explore. The alternative of performing a screening of the variables individually can provide certain insight about the required precision of variables, but, on the other hand, other complex interactions that involve several variables may remain hidden. Instead, we use a divide-and-conquer algorithm that identifies the parts that require high precision and establishes a set of variables that can handle reduced precision. This method has been tested using two state-of-the-art ocean models, the Nucleus for European Modelling of the Ocean (NEMO) and the Regional Ocean Modeling System (ROMS), with very promising results. Obtaining this information is crucial to build an actual mixed-precision version of the code in the next phase that will bring the promised performance benefits.

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Copper-dependent ATP7B up-regulation drives the resistance of TMEM16A-overexpressing head-and-neck cancer models to platinum toxicity

Biochemical Journal ◽

10.1042/bcj20190591 ◽

2019 ◽

Vol 476 (24) ◽

pp. 3705-3719 ◽

Cited By ~ 2

Author(s):

Avani Vyas ◽

Umamaheswar Duvvuri ◽

Kirill Kiselyov

Keyword(s):

Oxidative Stress ◽

Head And Neck ◽

Transcriptional Activation ◽

Platinum Resistance ◽

Mrna Levels ◽

Strong Positive Correlation ◽

Platinum Compounds ◽

Copper Chelation ◽

Novel Approach ◽

Cancer Models

Platinum-containing drugs such as cisplatin and carboplatin are routinely used for the treatment of many solid tumors including squamous cell carcinoma of the head and neck (SCCHN). However, SCCHN resistance to platinum compounds is well documented. The resistance to platinum has been linked to the activity of divalent transporter ATP7B, which pumps platinum from the cytoplasm into lysosomes, decreasing its concentration in the cytoplasm. Several cancer models show increased expression of ATP7B; however, the reason for such an increase is not known. Here we show a strong positive correlation between mRNA levels of TMEM16A and ATP7B in human SCCHN tumors. TMEM16A overexpression and depletion in SCCHN cell lines caused parallel changes in the ATP7B mRNA levels. The ATP7B increase in TMEM16A-overexpressing cells was reversed by suppression of NADPH oxidase 2 (NOX2), by the antioxidant N-Acetyl-Cysteine (NAC) and by copper chelation using cuprizone and bathocuproine sulphonate (BCS). Pretreatment with either chelator significantly increased cisplatin's sensitivity, particularly in the context of TMEM16A overexpression. We propose that increased oxidative stress in TMEM16A-overexpressing cells liberates the chelated copper in the cytoplasm, leading to the transcriptional activation of ATP7B expression. This, in turn, decreases the efficacy of platinum compounds by promoting their vesicular sequestration. We think that such a new explanation of the mechanism of SCCHN tumors’ platinum resistance identifies novel approach to treating these tumors.

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Collecting Words: A Clinical Example of a Morphology-Focused Orthographic Intervention

Language Speech and Hearing Services in Schools ◽

10.1044/2020_lshss-19-00050 ◽

2020 ◽

Vol 51 (3) ◽

pp. 544-560 ◽

Cited By ~ 3

Author(s):

Kimberly A. Murphy ◽

Emily A. Diehm

Keyword(s):

Written Language ◽

Morphological Knowledge ◽

English Orthography ◽

Word Level ◽

Novel Approach ◽

Language Pathology ◽

The One ◽

Critical Intervention ◽

Reading And Spelling ◽

Reading And Spelling Difficulties

Purpose Morphological interventions promote gains in morphological knowledge and in other oral and written language skills (e.g., phonological awareness, vocabulary, reading, and spelling), yet we have a limited understanding of critical intervention features. In this clinical focus article, we describe a relatively novel approach to teaching morphology that considers its role as the key organizing principle of English orthography. We also present a clinical example of such an intervention delivered during a summer camp at a university speech and hearing clinic. Method Graduate speech-language pathology students provided a 6-week morphology-focused orthographic intervention to children in first through fourth grade ( n = 10) who demonstrated word-level reading and spelling difficulties. The intervention focused children's attention on morphological families, teaching how morphology is interrelated with phonology and etymology in English orthography. Results Comparing pre- and posttest scores, children demonstrated improvement in reading and/or spelling abilities, with the largest gains observed in spelling affixes within polymorphemic words. Children and their caregivers reacted positively to the intervention. Therefore, data from the camp offer preliminary support for teaching morphology within the context of written words, and the intervention appears to be a feasible approach for simultaneously increasing morphological knowledge, reading, and spelling. Conclusion Children with word-level reading and spelling difficulties may benefit from a morphology-focused orthographic intervention, such as the one described here. Research on the approach is warranted, and clinicians are encouraged to explore its possible effectiveness in their practice. Supplemental Material https://doi.org/10.23641/asha.12290687

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