scholarly journals Parallel I∕O in Flexible Modelling System (FMS) and Modular Ocean Model 5 (MOM5)

2020 ◽  
Vol 13 (4) ◽  
pp. 1885-1902
Author(s):  
Rui Yang ◽  
Marshall Ward ◽  
Ben Evans
Keyword(s):  
Ocean Model ◽  
Tuning Parameters ◽  
Performance Improvements ◽  
Climate Forecasting ◽  
Single File ◽  
Model Configuration ◽  
Numerical Ocean Model ◽  
Resolution Model ◽  
Modular Ocean Model ◽  
Modelling System

Abstract. We present an implementation of parallel I∕O in the Modular Ocean Model (MOM), a numerical ocean model used for climate forecasting, and determine its optimal performance over a range of tuning parameters. Our implementation uses the parallel API of the netCDF library, and we investigate the potential bottlenecks associated with the model configuration, netCDF implementation, the underpinning MPI-IO library/implementations and Lustre filesystem. We investigate the performance of a global 0.25∘ resolution model using 240 and 960 CPUs. The best performance is observed when we limit the number of contiguous I∕O domains on each compute node and assign one MPI rank to aggregate and to write the data from each node, while ensuring that all nodes participate in writing this data to our Lustre filesystem. These best-performance configurations are then applied to a higher 0.1∘ resolution global model using 720 and 1440 CPUs, where we observe even greater performance improvements. In all cases, the tuned parallel I∕O implementation achieves much faster write speeds relative to serial single-file I∕O, with write speeds up to 60 times faster at higher resolutions. Under the constraints outlined above, we observe that the performance scales as the number of compute nodes and I∕O aggregators are increased, ensuring the continued scalability of I∕O-intensive MOM5 model runs that will be used in our next-generation higher-resolution simulations.

scholarly journals Parallel I/O in FMS and MOM5

2019 ◽  
Author(s):  
Rui Yang ◽  
Marshall Ward ◽  
Ben Evans
Keyword(s):  
Ocean Model ◽  
Global Model ◽  
Tuning Parameters ◽  
Performance Improvements ◽  
Climate Forecasting ◽  
Single File ◽  
Model Configuration ◽  
Numerical Ocean Model ◽  
Resolution Model ◽  
Modular Ocean Model

Abstract. We present an implementation of parallel I/O in the Modular Ocean Model (MOM), a numerical ocean model used for climate forecasting, and determine its optimal performance over a range of tuning parameters. Our implementation uses the parallel API of the netCDF library, and we investigate the potential bottlenecks associated with the model configuration, netCDF implementation, the underpinning MPI-IO library/implementations and Lustre filesystem. We investigate the performance of a global 0.25° resolution model using 240 and 960 CPUs. The best performance is observed when we limit the number of contiguous I/O domains on each compute node and assign one MPI rank to aggregate and write the data from each node, while ensuring that all nodes participate in writing this data to our Lustre filesystem. These best performance configurations are then applied to a higher 0.1° resolution global model using 720 and 1440 CPUs, where we observe even greater performance improvements. In all cases, the tuned parallel I/O implementation achieves much faster write speeds relative to serial single-file I/O, with write speeds up to 60 times faster at higher resolutions. Under the constraints outlined above, we observe that the performance scales as the number of compute nodes and I/O aggregators are increased, ensuring the continued scalability of I/O-intensive MOM5 model runs that will be used in our next generation higher resolution simulations.

scholarly journals MOMSO 1.0 – an eddying Southern Ocean model configuration with fairly equilibrated natural carbon

2020 ◽  
Vol 13 (1) ◽  
pp. 71-97
Author(s):  
Heiner Dietze ◽  
Ulrike Löptien ◽  
Julia Getzlaff
Keyword(s):  
Southern Ocean ◽  
Ocean Circulation ◽  
Solid Wall ◽  
Computational Cost ◽  
Circulation Model ◽  
Ocean Model ◽  
Geophysical Fluid Dynamics Laboratory ◽  
Sensitivity Experiment ◽  
Model Configuration ◽  
Modular Ocean Model

Abstract. We present a new near-global coupled biogeochemical ocean-circulation model configuration. The configuration features a horizontal discretization with a grid spacing of less than 11 km in the Southern Ocean and gradually coarsens in meridional direction to more than 200 km at 64∘ N, where the model is bounded by a solid wall. The underlying code framework is the Geophysical Fluid Dynamics Laboratory (GFDL)'s Modular Ocean Model coupled to the Biogeochemistry with Light, Iron, Nutrients and Gases (BLING) ecosystem model of Galbraith et al. (2010). The configuration is unique in that it features both a relatively equilibrated oceanic carbon inventory and an eddying ocean circulation based on a realistic model geometry/bathymetry – a combination that has been precluded by prohibitive computational cost in the past. Results from a simulation with climatological forcing and a sensitivity experiment with increasing winds suggest that the configuration is sufficiently equilibrated to explore Southern Ocean carbon uptake dynamics on decadal timescales. The configuration is dubbed MOMSO, a Modular Ocean Model Southern Ocean configuration.

scholarly journals MOMSO 1.0 - a near-global, coupled biogeochemical ocean-circulation model configuration with realistic eddy kinetic energy in the Southern Ocean

2019 ◽  
Author(s):  
Heiner Dietze ◽  
Ulrike Löptien ◽  
Julia Getzlaff
Keyword(s):  
Kinetic Energy ◽  
Southern Ocean ◽  
Ocean Circulation ◽  
Computational Cost ◽  
Circulation Model ◽  
Ocean Model ◽  
Eddy Kinetic Energy ◽  
Ocean Circulation Model ◽  
Model Configuration ◽  
Modular Ocean Model

Abstract. We present a new near-global coupled biogeochemical ocean-circulation model configuration. The configuration features a horizontal discretization with a grid spacing of less than 11 km in the Southern Ocean and gradually coarsens in meridional direction to more than 200 km at 64° N where the model is bounded by a solid wall. The underlying code framework is GFDL's Modular Ocean Model coupled to the Biology Light Iron Nutrients and Gasses (BLING) ecosystem model of Galbraith et al. (2010). The configuration is cutting-edge in that it features both a relatively equilibrated oceanic carbon inventory and a realistic representation of eddy kinetic energy – a combination that has, to-date, been precluded by prohibitive computational cost. Results from a simulation with climatological forcing and a sensitivity experiment with increasing winds suggest that the configuration is suited to explore Southern Ocean Carbon uptake dynamics on decadal timescales. Further, the fidelity of simulated bottom water temperatures off and on the Antarctic Shelf suggest that the configuration may be used to provide boundary conditions to ice-sheet models. The configuration is dubbed MOMSO a Modular Ocean Model Southern Ocean configuration.

scholarly journals Modelling dispersal of eggs and quantifying connectivity among Norwegian coastal cod subpopulations

2013 ◽  
Vol 71 (4) ◽  
pp. 957-969 ◽  
Author(s):  
Mari S. Myksvoll ◽  
Kyung-Mi Jung ◽  
Jon Albretsen ◽  
Svein Sundby
Keyword(s):  
Ocean Model ◽  
Small Scale ◽  
Coastal Current ◽  
Life Stages ◽  
Early Life Stages ◽  
Dispersal Patterns ◽  
Norwegian Coast ◽  
Spawning Areas ◽  
Numerical Ocean Model ◽  
Norwegian Coastal Current

Abstract The Norwegian coast is populated by two cod populations: Northeast Arctic cod and Norwegian Coastal cod. In this paper, we use a further division based on life history: oceanic cod, coastal cod, and fjord cod. A numerical ocean model was implemented for the northern Norwegian coast where all these populations have spawning areas. The model results were used to simulate connectivity and retention of cod eggs from the different subpopulations. The model reproduced the observed variability and mesoscale activity in the Norwegian Coastal Current. Eggs released at an oceanic spawning area were transported northwards along the coastline. Coastal cod eggs had intermediate connectivity with each other and fjord cod eggs had high local retention. Although the high retention of eggs in fjord areas is mainly caused by a subsurface distribution of eggs, the intermediate retention of eggs from coastal spawning areas is caused by small-scale eddies in-between many small islands. The high-resolution ocean model made it possible to reveal these specific dispersal patterns. The high retention of early life stages in fjords combined with strong homing to spawning areas indicates that fjord subpopulations may be described as a metapopulation.

Detecting and characterizing upwelling filaments in a numerical ocean model

2019 ◽  
Vol 122 ◽  
pp. 25-34 ◽  
Author(s):  
Osvaldo Artal ◽  
Héctor H. Sepúlveda ◽  
Domingo Mery ◽  
Christian Pieringer
Keyword(s):  
Ocean Model ◽  
Numerical Ocean Model

scholarly journals Central Mediterranean Sea forecast: effects of high-resolution atmospheric forcings

2006 ◽  
Vol 3 (3) ◽  
pp. 637-669 ◽  
Author(s):  
S. Natale ◽  
R. Sorgente ◽  
S. Gaberšek ◽  
A. Ribotti ◽  
A. Olita
Keyword(s):  
High Resolution ◽  
Ocean Circulation ◽  
Regional Scale ◽  
Circulation Model ◽  
Surface Current ◽  
Ocean Model ◽  
Central Mediterranean ◽  
Resolution Model ◽  
Atmospheric Forcings ◽  
Very High

Abstract. Ocean forecasts over the Central Mediterranean, produced by a near real time regional scale system, have been evaluated in order to assess their predictability. The ocean circulation model has been forced at the surface by a medium, high or very high resolution atmospheric forcing. The simulated ocean parameters have been compared with satellite data and they were found to be generally in good agreement. High and very high resolution atmospheric forcings have been able to form noticeable, although short-lived, surface current structures, due to their ability to detect transient atmospheric disturbances. The existence of the current structures has not been directly assessed due to lack of measurements. The ocean model in the slave mode was not able to develop dynamics different from the driving coarse resolution model which provides the boundary conditions.

scholarly journals RELAÇÃO ENTRE A TEMPERATURA DA SUPERFÍCIE DO MAR E A CAMADA DE MISTURA OCEÂNICA SOB A PASSAGEM DE CICLONES EXTRATROPICAIS NO ATLÂNTICO SUDOESTE

2015 ◽  
Vol 30 (1) ◽  
pp. 89-100 ◽  
Author(s):  
Ana Cristina Pinto de Almeida Palmeira ◽  
Ricardo de Camargo ◽  
Ronaldo Maia de Jesus Palmeira
Keyword(s):  
Ocean Model ◽  
Atmospheric Modelling ◽  
Regional Atmospheric Modelling System ◽  
Hybrid Coordinate Ocean Model ◽  
Modelling System

Neste artigo investigou-se a importância da variação da camada de mistura oceânica (CMO) na temperatura da superfície do mar (TSM), sob a influencia de ciclones extratropicais atmosféricos. Um modelo simplificado de CMO oriundo do modelo HYCOM (Hybrid Coordinate Ocean Model), baseado no modelo de Kraus e Turner, foi inserido como uma sub-rotina do modelo BRAMS (Brazilian Regional Atmospheric Modelling System), para atualizar a TSM a cada passo de tempo no modelo atmosférico. A CMO-BRAMS caracterizou-se por estreitar durante as trajetórias das baixas pressões, embora não tenha indicado um significativo aprofundamento seguindo o anticiclone da retaguarda do sistema frontal. A TSM calculada pela CMO do BRAMS apresentou grande variação (1°C-5°C) nos instantes iniciais. Entretanto, uma vez ajustada houve pouca variação da TSM no decorrer do tempo (1,0°C-2,5°C), com o aprofundamento (estreitamento) da CMO associada à diminuição (aumento) à temperatura.

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