Roger Proctor - Academia.edu (original) (raw)

Papers by Roger Proctor

Research paper thumbnail of Advective controls on primary production in the stratified western Irish Sea: An eddy-resolving model study

1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional... more 1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional Seas Ecosystem Model are applied at eddy-resolving ($1.8 km) scales to the stratified region of the western Irish Sea to investigate the effects of advective transport processes on the ecosystem. We find currents can transport nutrient-rich water into the otherwise nutrient-depleted surface layer of the stratified region, fueling intermittent production throughout the summer. The currents involved fall into three classes: large-scale wind and density-driven circulation, smaller-scale eddies, and tidally mediated dispersive phenomena; all appear to play a role in this area. A model experiment without ecosystem advection does not show the intermittent surface production; summer growth only occurs at the thermocline. This experiment gives a significantly lower total annual production of 110 ± 26 g C m À2 yr À1 , compared with 150 ± 40 g C m À2 yr À1 for the full model, which is in better agreement with observational estimates of 140 g C m À2 yr À1 . We calculate summer averages of the terms in the scalar transport equation, which show that advective transport of all nutrients dominates over vertical diffusion above the thermocline in most of the stratified region. The transport of nitrate, ammonia, and phosphate is significantly greater than the transport of silicate. This can be attributed to the lack of silicate recycling in the pelagic ecosystem. Only limited and anecdotal observational evidence exists to support these model results, which points to a need for observations of high spatial and temporal resolution to investigate these processes in conjunction with further model studies.

Research paper thumbnail of A highly spatially resolved ecosystem model for the North West European Continental Shelf

Sarsia, 2001

Siddorn J. 2001. A highly spatially resolved ecosystem model for the North West European Continen... more Siddorn J. 2001. A highly spatially resolved ecosystem model for the North West European Continental Shelf. Sarsia 86:423-440.

Research paper thumbnail of Modelling the global coastal ocean

Philosophical Transactions of The Royal Society A: Mathematical, Physical and Engineering Sciences, 2009

Research paper thumbnail of EDDY RESOLVED ECOSYSTEM MODELLING IN THE IRISH SEA

A computationally efficient three-dimensional modelling system (Proudman Oceanographic Laboratory... more A computationally efficient three-dimensional modelling system (Proudman Oceanographic Laboratory Coastal-Ocean Modelling System, POLCOMS) has been developed for the simulation of shelf-sea, ocean and coupled shelf-ocean processes. The system is equally suited for use on single processor workstations and massively parallel supercomputers, and particular features of its numerics are an arbitrary (terrain following) vertical coordinate system, a feature preserving advection scheme and accurate calculation of horizontal pressure gradients, even in the presence of steep topography.

Research paper thumbnail of Optimization of the POLCOMS Hydrodynamic Code for Terascale High-Performance Computers

Advances in computational science are closely tied to developments in highperformance computing. ... more Advances in computational science are closely tied to developments in highperformance computing. We consider the case of shelf sea modelling where models have been growing in complexity and where model domains have been growing and grid resolutions shrinking in pace with the increasing storage capacity and computing power of high-end systems. Terascale systems are now readily available with performance levels measurable in TeraFlop/s and memories counted in TeraBytes. The scientific case is now being made for regional models at 1km resolution, allowing the accurate representation of eddies, fronts and other regions containing steep gradients. The hydrodynamic model is increasingly being coupled with other models in multidisciplinary studies e.g. ecosystem modelling and wave modelling. We show that the performance attainable from the POLCOMS hydrodynamic code is measurable at about 0.5 TeraFlop/s on an IBM p690 cluster with 1024 processors. The scalability on this system and others is excellent up to 1000 processors. We describe a wide range of optimisations which have together enabled this code to reach these performance levels.

Research paper thumbnail of Coupled marine ecosystem modelling on high-performance computers

Research paper thumbnail of Advective controls on primary production in the stratified western Irish Sea: An eddy-resolving model study

Journal of Geophysical Research, 2004

1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional... more 1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional Seas Ecosystem Model are applied at eddy-resolving ($1.8 km) scales to the stratified region of the western Irish Sea to investigate the effects of advective transport processes on the ecosystem. We find currents can transport nutrient-rich water into the otherwise nutrient-depleted surface layer of the stratified region, fueling intermittent production throughout the summer. The currents involved fall into three classes: large-scale wind and density-driven circulation, smaller-scale eddies, and tidally mediated dispersive phenomena; all appear to play a role in this area. A model experiment without ecosystem advection does not show the intermittent surface production; summer growth only occurs at the thermocline. This experiment gives a significantly lower total annual production of 110 ± 26 g C m À2 yr À1 , compared with 150 ± 40 g C m À2 yr À1 for the full model, which is in better agreement with observational estimates of 140 g C m À2 yr À1 . We calculate summer averages of the terms in the scalar transport equation, which show that advective transport of all nutrients dominates over vertical diffusion above the thermocline in most of the stratified region. The transport of nitrate, ammonia, and phosphate is significantly greater than the transport of silicate. This can be attributed to the lack of silicate recycling in the pelagic ecosystem. Only limited and anecdotal observational evidence exists to support these model results, which points to a need for observations of high spatial and temporal resolution to investigate these processes in conjunction with further model studies.

Research paper thumbnail of Mind the Gap: furthering the development of an international collaboration in marine data management

Research paper thumbnail of Ocean Data Interoperability Platform (ODIP): developing an international collaboration in marine data management

Research paper thumbnail of Australia’s Interface to Open Access Marine Data

The waters surrounding the Australian island continent are significantly important, affecting cli... more The waters surrounding the Australian island continent are significantly important, affecting climate, industry, economy, tourism, and lifestyle. In fact, despite its enormous landmass, 90% of Australia's population of 22 million live within 120 km of the coast! Australian waters have been ranked as the biologically most diverse by the recent Census of Marine Life, with 80% of species still unknown. Access to a variety of marine data – physical, biogeochemical, and biological – therefore should be the interest and the right of everyone. The reality is, however, that data is hardly ever shared with stakeholders outside of the respective research institution or governmental department. Due to this lack of cross-sector communication, “knowledge gaps” are less likely to be identified and duplication of effort in data collection and analysis is common. A subset of publicly funded marine data is currently available through the information infrastructure of the Integrated Marine Observ...

Research paper thumbnail of Baroclinic Features In The Irish Sea: Modelling Their Impact On Primary Production

Egs General Assembly Conference Abstracts, 2002

Seasonal cycles in the Irish Sea have been simulated with a 3-dimensional hydrody- namic model ca... more Seasonal cycles in the Irish Sea have been simulated with a 3-dimensional hydrody- namic model capable of resolving the internal baroclinic radius of deformation. The main features of the hydrodynamics are reproduced, most notably the thermally strat- ifed 'gyre' region west of the Isle of Man and the associated tidal fronts. Ecosystem dynamics have been coupled to the hydrodynamics with the emphasis on primary production. Additional 1-dimensional coupled model experiments indicate the role that the 3-dimensional baroclinic processes play in determining primary production and show why 1-dimensional model simulations need to be treated with care in areas where baroclinic currents exist.

Research paper thumbnail of Modelling the inter-annual variability of carbon fluxes and budgets on the northwest European continental shelf

Research paper thumbnail of High-resolution modelling of the Northwest European shelf seas using POLCOMS

Research paper thumbnail of Coupled Marine Ecosystem Modelling on High-Performance Computers M. Ashworth

Research paper thumbnail of Eddy resolved ecosystem modelling in the Irish Sea: Advective controls of primary production

The Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) has been coupled t... more The Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) has been coupled to the European Region Seas Ecosystem Model (ERSEM) and applied to the Irish Sea at a resolution of ~1.8km, to explore the detailed interaction between physical and biological processes in both horizontal and vertical. This grid size allows all the dominant physical scales (the tidal excursion, the baroclinic Rossby radius and the wavelength of M2 internal tide) to be resolved. Investigations with the physics-only model show the significance of advective processes (particularly large scale currents, shear diffusion and baroclinic eddies) in determining the vertical and horizontal temperature structure in this region. Here we investigate how these processes affect the evolution and horizontal distribution of phytoplankton (and primary production) and nutrients predicted by the ecosystem model, demonstrating that cross-frontal nutrient transport can fuel sporadic surface production throughout the summer in the stratified region. This production does not occur without the advective component of the ecosystem model and accounts for ~50% of the total annual production. The model results are compared with Seawifs and in-situ observations to assess their validity.

Research paper thumbnail of The National Centre for Ocean Forecasting

Research paper thumbnail of Forecasting ecosystem status in shelf seas (MERSEA)

An objective of MERSEA is to demonstrate that products pertinent to the assessment of the eutroph... more An objective of MERSEA is to demonstrate that products pertinent to the assessment of the eutrophic status of marine systems can be produced in near real time and to assess the usefulness of such products. This will be carried out by running in near real time the POLCOMS North West European shelf ecosystem model. The system can produce forecasts of

Research paper thumbnail of Supplementary Information The thermohaline circulation of shallow tidal seas

Research paper thumbnail of Towards the assessment and demonstration of the value of GODAE results for coastal and shelf seas models and forecasting systems

Research paper thumbnail of The Synthesis of Modeling and Measurements in a Coastal Observatory

The pilot Coastal Observatory in the eastern Irish Sea integrates (near) real-time measurements w... more The pilot Coastal Observatory in the eastern Irish Sea integrates (near) real-time measurements with coupled models in a pre-operational coastal prediction system. The aim is to develop the underpinning science for marine management, focusing on the impacts of storms, eutrophication and the relative importance of events viz-a-viz the mean. Real time current measurements are obtained from a sea-bed mounted Acoustic Doppler Current Profiler, deployment started in August 2002, via acoustic modems and the Orbcomm satellite e-mail system, and from a shore based HF radar via telephone landlines. There are also real time measurements from a surface buoy and a directional wave buoy and from an instrumented ferry, all via Orbcomm. The measurements are integrated with a suite of nested 3-dimensional hydrodynamic and ecological models run daily, focusing on the Observatory area by covering the ocean / shelf of northwest Europe (at 12 km resolution), the Irish Sea (at 1.8 km) and Liverpool Bay (at 200-300m resolution). All measurements and model outputs are displayed on the website (http://coastobs.pol.ac.uk).

Research paper thumbnail of Advective controls on primary production in the stratified western Irish Sea: An eddy-resolving model study

1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional... more 1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional Seas Ecosystem Model are applied at eddy-resolving ($1.8 km) scales to the stratified region of the western Irish Sea to investigate the effects of advective transport processes on the ecosystem. We find currents can transport nutrient-rich water into the otherwise nutrient-depleted surface layer of the stratified region, fueling intermittent production throughout the summer. The currents involved fall into three classes: large-scale wind and density-driven circulation, smaller-scale eddies, and tidally mediated dispersive phenomena; all appear to play a role in this area. A model experiment without ecosystem advection does not show the intermittent surface production; summer growth only occurs at the thermocline. This experiment gives a significantly lower total annual production of 110 ± 26 g C m À2 yr À1 , compared with 150 ± 40 g C m À2 yr À1 for the full model, which is in better agreement with observational estimates of 140 g C m À2 yr À1 . We calculate summer averages of the terms in the scalar transport equation, which show that advective transport of all nutrients dominates over vertical diffusion above the thermocline in most of the stratified region. The transport of nitrate, ammonia, and phosphate is significantly greater than the transport of silicate. This can be attributed to the lack of silicate recycling in the pelagic ecosystem. Only limited and anecdotal observational evidence exists to support these model results, which points to a need for observations of high spatial and temporal resolution to investigate these processes in conjunction with further model studies.

Research paper thumbnail of A highly spatially resolved ecosystem model for the North West European Continental Shelf

Sarsia, 2001

Siddorn J. 2001. A highly spatially resolved ecosystem model for the North West European Continen... more Siddorn J. 2001. A highly spatially resolved ecosystem model for the North West European Continental Shelf. Sarsia 86:423-440.

Research paper thumbnail of Modelling the global coastal ocean

Philosophical Transactions of The Royal Society A: Mathematical, Physical and Engineering Sciences, 2009

Research paper thumbnail of EDDY RESOLVED ECOSYSTEM MODELLING IN THE IRISH SEA

A computationally efficient three-dimensional modelling system (Proudman Oceanographic Laboratory... more A computationally efficient three-dimensional modelling system (Proudman Oceanographic Laboratory Coastal-Ocean Modelling System, POLCOMS) has been developed for the simulation of shelf-sea, ocean and coupled shelf-ocean processes. The system is equally suited for use on single processor workstations and massively parallel supercomputers, and particular features of its numerics are an arbitrary (terrain following) vertical coordinate system, a feature preserving advection scheme and accurate calculation of horizontal pressure gradients, even in the presence of steep topography.

Research paper thumbnail of Optimization of the POLCOMS Hydrodynamic Code for Terascale High-Performance Computers

Advances in computational science are closely tied to developments in highperformance computing. ... more Advances in computational science are closely tied to developments in highperformance computing. We consider the case of shelf sea modelling where models have been growing in complexity and where model domains have been growing and grid resolutions shrinking in pace with the increasing storage capacity and computing power of high-end systems. Terascale systems are now readily available with performance levels measurable in TeraFlop/s and memories counted in TeraBytes. The scientific case is now being made for regional models at 1km resolution, allowing the accurate representation of eddies, fronts and other regions containing steep gradients. The hydrodynamic model is increasingly being coupled with other models in multidisciplinary studies e.g. ecosystem modelling and wave modelling. We show that the performance attainable from the POLCOMS hydrodynamic code is measurable at about 0.5 TeraFlop/s on an IBM p690 cluster with 1024 processors. The scalability on this system and others is excellent up to 1000 processors. We describe a wide range of optimisations which have together enabled this code to reach these performance levels.

Research paper thumbnail of Coupled marine ecosystem modelling on high-performance computers

Research paper thumbnail of Advective controls on primary production in the stratified western Irish Sea: An eddy-resolving model study

Journal of Geophysical Research, 2004

1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional... more 1] The Proudman Oceanographic Laboratory Coastal Ocean Modelling System and the European Regional Seas Ecosystem Model are applied at eddy-resolving ($1.8 km) scales to the stratified region of the western Irish Sea to investigate the effects of advective transport processes on the ecosystem. We find currents can transport nutrient-rich water into the otherwise nutrient-depleted surface layer of the stratified region, fueling intermittent production throughout the summer. The currents involved fall into three classes: large-scale wind and density-driven circulation, smaller-scale eddies, and tidally mediated dispersive phenomena; all appear to play a role in this area. A model experiment without ecosystem advection does not show the intermittent surface production; summer growth only occurs at the thermocline. This experiment gives a significantly lower total annual production of 110 ± 26 g C m À2 yr À1 , compared with 150 ± 40 g C m À2 yr À1 for the full model, which is in better agreement with observational estimates of 140 g C m À2 yr À1 . We calculate summer averages of the terms in the scalar transport equation, which show that advective transport of all nutrients dominates over vertical diffusion above the thermocline in most of the stratified region. The transport of nitrate, ammonia, and phosphate is significantly greater than the transport of silicate. This can be attributed to the lack of silicate recycling in the pelagic ecosystem. Only limited and anecdotal observational evidence exists to support these model results, which points to a need for observations of high spatial and temporal resolution to investigate these processes in conjunction with further model studies.

Research paper thumbnail of Mind the Gap: furthering the development of an international collaboration in marine data management

Research paper thumbnail of Ocean Data Interoperability Platform (ODIP): developing an international collaboration in marine data management

Research paper thumbnail of Australia’s Interface to Open Access Marine Data

The waters surrounding the Australian island continent are significantly important, affecting cli... more The waters surrounding the Australian island continent are significantly important, affecting climate, industry, economy, tourism, and lifestyle. In fact, despite its enormous landmass, 90% of Australia's population of 22 million live within 120 km of the coast! Australian waters have been ranked as the biologically most diverse by the recent Census of Marine Life, with 80% of species still unknown. Access to a variety of marine data – physical, biogeochemical, and biological – therefore should be the interest and the right of everyone. The reality is, however, that data is hardly ever shared with stakeholders outside of the respective research institution or governmental department. Due to this lack of cross-sector communication, “knowledge gaps” are less likely to be identified and duplication of effort in data collection and analysis is common. A subset of publicly funded marine data is currently available through the information infrastructure of the Integrated Marine Observ...

Research paper thumbnail of Baroclinic Features In The Irish Sea: Modelling Their Impact On Primary Production

Egs General Assembly Conference Abstracts, 2002

Seasonal cycles in the Irish Sea have been simulated with a 3-dimensional hydrody- namic model ca... more Seasonal cycles in the Irish Sea have been simulated with a 3-dimensional hydrody- namic model capable of resolving the internal baroclinic radius of deformation. The main features of the hydrodynamics are reproduced, most notably the thermally strat- ifed 'gyre' region west of the Isle of Man and the associated tidal fronts. Ecosystem dynamics have been coupled to the hydrodynamics with the emphasis on primary production. Additional 1-dimensional coupled model experiments indicate the role that the 3-dimensional baroclinic processes play in determining primary production and show why 1-dimensional model simulations need to be treated with care in areas where baroclinic currents exist.

Research paper thumbnail of Modelling the inter-annual variability of carbon fluxes and budgets on the northwest European continental shelf

Research paper thumbnail of High-resolution modelling of the Northwest European shelf seas using POLCOMS

Research paper thumbnail of Coupled Marine Ecosystem Modelling on High-Performance Computers M. Ashworth

Research paper thumbnail of Eddy resolved ecosystem modelling in the Irish Sea: Advective controls of primary production

The Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) has been coupled t... more The Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) has been coupled to the European Region Seas Ecosystem Model (ERSEM) and applied to the Irish Sea at a resolution of ~1.8km, to explore the detailed interaction between physical and biological processes in both horizontal and vertical. This grid size allows all the dominant physical scales (the tidal excursion, the baroclinic Rossby radius and the wavelength of M2 internal tide) to be resolved. Investigations with the physics-only model show the significance of advective processes (particularly large scale currents, shear diffusion and baroclinic eddies) in determining the vertical and horizontal temperature structure in this region. Here we investigate how these processes affect the evolution and horizontal distribution of phytoplankton (and primary production) and nutrients predicted by the ecosystem model, demonstrating that cross-frontal nutrient transport can fuel sporadic surface production throughout the summer in the stratified region. This production does not occur without the advective component of the ecosystem model and accounts for ~50% of the total annual production. The model results are compared with Seawifs and in-situ observations to assess their validity.

Research paper thumbnail of The National Centre for Ocean Forecasting

Research paper thumbnail of Forecasting ecosystem status in shelf seas (MERSEA)

An objective of MERSEA is to demonstrate that products pertinent to the assessment of the eutroph... more An objective of MERSEA is to demonstrate that products pertinent to the assessment of the eutrophic status of marine systems can be produced in near real time and to assess the usefulness of such products. This will be carried out by running in near real time the POLCOMS North West European shelf ecosystem model. The system can produce forecasts of

Research paper thumbnail of Supplementary Information The thermohaline circulation of shallow tidal seas

Research paper thumbnail of Towards the assessment and demonstration of the value of GODAE results for coastal and shelf seas models and forecasting systems

Research paper thumbnail of The Synthesis of Modeling and Measurements in a Coastal Observatory

The pilot Coastal Observatory in the eastern Irish Sea integrates (near) real-time measurements w... more The pilot Coastal Observatory in the eastern Irish Sea integrates (near) real-time measurements with coupled models in a pre-operational coastal prediction system. The aim is to develop the underpinning science for marine management, focusing on the impacts of storms, eutrophication and the relative importance of events viz-a-viz the mean. Real time current measurements are obtained from a sea-bed mounted Acoustic Doppler Current Profiler, deployment started in August 2002, via acoustic modems and the Orbcomm satellite e-mail system, and from a shore based HF radar via telephone landlines. There are also real time measurements from a surface buoy and a directional wave buoy and from an instrumented ferry, all via Orbcomm. The measurements are integrated with a suite of nested 3-dimensional hydrodynamic and ecological models run daily, focusing on the Observatory area by covering the ocean / shelf of northwest Europe (at 12 km resolution), the Irish Sea (at 1.8 km) and Liverpool Bay (at 200-300m resolution). All measurements and model outputs are displayed on the website (http://coastobs.pol.ac.uk).