Mike Ashworth

A highly spatially resolved ecosystem model for the North West European Continental Shelf

Abstract This paper outlines an approach to complex spatio-temporal marine ecosystem modelling as applied to the North Western European Continental Shelf. The model presented here goes further than previous work, as we combine a higher resolution hydrodynamic model, the POL-3DB baroclinic model with the European Regional Seas Ecosystem Model. This combination of models includes many of the processes (benthic-pelagic coupling, dynamic zooplankton and nitrogen, phosphorous and silicate cycling) previous authors have identitied as missing from their models and partially responsible for the inadequacies of their simulations. Spatial distributions of key physical and ecological variables taken from the three dimensional high resolution hydrodynamic/ecological simulations are presented to illustrate how spatial and temporal variations in physical processes determine the onset of the spring bloom in the North Sea. A basic validation of these simulations is presented, which indicates the model reproduces many of the features of the seasonal cycles of nutrients and phytoplankton, but fails to simulate mesozooplankton biomass in a convincing manner. The reasons for this are discussed along with potential new research directions.

Modelling the global coastal ocean

Shelf and coastal seas are regions of exceptionally high biological productivity, high rates of biogeochemical cycling and immense socio-economic importance. They are, however, poorly represented by the present generation of Earth system models, both in terms of resolution and process representation. Hence, these models cannot be used to elucidate the role of the coastal ocean in global biogeochemical cycles and the effects global change (both direct anthropogenic and climatic) are having on them. Here, we present a system for simulating all the coastal regions around the world (the Global Coastal Ocean Modelling System) in a systematic and practical fashion. It is based on automatically generating multiple nested model domains, using the Proudman Oceanographic Laboratory Coastal Ocean Modelling System coupled to the European Regional Seas Ecosystem Model. Preliminary results from the system are presented. These demonstrate the viability of the concept, and we discuss the prospects for using the system to explore key areas of global change in shelf seas, such as their role in the carbon cycle and climate change effects on fisheries.

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 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 -2 yr -1 , compared with 150 ± 40 g C m -2 yr -1 for the full model, which is in better agreement with observational estimates of 140 g C m-2 yr -1 . 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.

Optimization of the POLCOMS hydrodynamic code for Terascale high-performance computers

Summary form only given. Advances in computational science are closely tied to developments in high-performance 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 1 km 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.

Low-Frequency 3D Wave Propagation Modeling of the 12 May 2008 Mw 7.9 Wenchuan Earthquake

The seismic potential of southern China is associated with the collision between the Indian and the Eurasian plates. This is manifested in the western Sichuan Plateau by several seismically active systems of faults, such as the Longmen Shan. The seismicity observed on the Longmen Shan fault includes recent events with magnitudes of up to 6.5, and the one of 12 May 2008 Mw 7.9 Wenchuan earth- quake. Herewith, as part of an ongoing research program, a recently optimized three- dimensional (3D) seismic wave propagation parallel finite-difference code was used to obtain low-frequency (≤ 0:3 Hz) 3D synthetic seismograms for the Wenchuan earthquake. The code was run on KanBalam (Universidad Nacional Autonoma de Mexico, Mexico) and HECToR (UK National Supercomputing Service) supercompu- ters. The modeling included the U.S. Geological Survey 40 × 315 km 2 kinematic description of the earthquakes rupture, embedded in a 2400 × 1600 × 300 km 3 phys- ical domain, spatially discretized at 1 km in the three directions and a temporal dis- cretization of 0.03 s. The compression and shear wave velocities and densities of the geologic structure used were obtained from recently published geophysical studies performed in the Sichuan region. The synthetic seismograms favorably compare with the observed ones for several station sites of the Seismological and Accelerographic Networks of China, such as MZQ, GYA, and TIY, located at about 90, 500, and 1200 km, respectively, from the epicenter of the Wenchuan event. Moreover, the com- parisons of synthetic displacements with differential radar interferometry (DinSAR) ground deformation imagery, as well as of maximum velocity synthetic patterns with Mercalli modified intensity isoseist of the 2008 Wenchuan earthquake, are acceptable. 3D visualizations of the propagation of the event were also obtained; they show the source rupture directivity effects of the Mw 7.9 Wenchuan event. Our results partially explain the extensive damage observed on the infrastructure and towns located in the neighborhood of the Wenchuan earthquake rupture zone.

Coupled Marine Ecosystem Modelling on High-Performance Computers

Simulation of the marine environment has become an important tool across a wide range of human activities, with applications in coastal engineering, offshore industries, fisheries management, marine pollution monitoring, weather forecasting and climate research to name but a few. Hydrodynamic models have been under development for many years and have reached a high level of sophistication. However, sustainable management of the ecological resources of coastal environments demands an ability to understand and predict the behaviour of the marine ecosystem. Thus, it is highly desirable to extend the capabilities of existing models to include chemical, bio-geo-chemical and biological processes within the marine ecosystem. This paper describes the development of a high-resolution threedimensional coupled transport/ecosystem model of the Northwest European continental shelf and explores the particular problems encountered in its implementation on high-performance computer systems. We present preliminary results from the coupled model. We also discuss the performance levels achieved and the parallelization and optimization strategies employed.

HPCx: towards capability computing

We introduce HPCx—the U.K.s new National HPC Service—which aims to deliver a world‐class service for capability computing to the U.K. scientific community. HPCx is targeting an environment that will both result in world‐leading science and address the challenges involved in scaling existing codes to the capability levels required. Close working relationships with scientific consortia and user groups throughout the research process will be a central feature of the service. A significant number of key user applications have already been ported to the system. We present initial benchmark results from this process and discuss the optimization of the codes and the performance levels achieved on HPCx in comparison with other systems. We find a range of performance with some algorithms scaling far better than others. Copyright

Parallelizing FLITE3D—a multigrid finite element Euler solver

FLITE3D is a multigrid Euler solver. It is used extensively by British Aerospace in aircraft design and simulation. This paper presents experiences in parallelizing this industrial code. Owing to the employment of an agglomeration-based multigrid technique, the communication overhead on the coarser meshes could readily erode any gain from the use of parallel computers. The parallelization of the code therefore required careful design and implementation. The strategy adopted in the parallelization of the code, including the use of data structures and communication primitives, is described. Numerical results are presented to demonstrate the efficiency of the resulting parallel code

Mapping application performance to HPC architecture

Abstract A suite of application benchmarks, designed to be broadly representative of UK HPC usage, has been developed to stress a broad range of architectural features of large scale parallel HPC resources. A generic methodology to investigate application performance and scaling characteristics has been defined, resulting in a detailed understanding of the performance of these applications. This methodology is transferable to other applications and systems: it is of practical value to developers and users who are aiming for optimal utilisation of HPC resources. An understanding of the performance characteristics of a range of large-scale HPC resources has been obtained using low-level synthetic benchmarks. A relatively simple, qualitative mechanism to assess and predict application performance on current and future architectures using synthetic benchmark results together with application performance analysis results is explored.

Eddy resolved ecosystem modelling in the Irish Sea

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. One of the roles of this system is to act as a host to ecosystem models, so that they can interact with as accurate a physical environment as is currently feasible. In this study, a hierarchy of nested models links the shelf-wide circulation and ecosystem, via a high resolution physics model of the whole Irish Sea, to the test domain: a region of the western Irish Sea. In this domain, ecosystem models are tested at a resolution of ~1.5km (c.f. the typical summer Rossby radius of 4km). Investigations in the physics-only model show the significance of advective processes (particularly shear diffusion and baroclinic eddies) in determining the vertical and horizontal temperature structure in this region. Here we investigate how a hierarchy of complexity (and computational load) from a 1D point model to a fully 3D eddy resolved model affects the distribution of phytoplankton (and primary production) and nutrients predicted by the European Regional Seas Ecosystem Model (ERSEM), a complex multi-compartment ecosystem model. We shall also show how the parallel programming features of the POLCOMS code allows large-scale simulations to be carried out on hundreds, and now on over a thousand, processors, approaching Teraflop/s performance levels. This is shown using a series of benchmark runs on the 1280 processor IBM POWER4 system operated by the UKs HPCx Consortium.