Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions

We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimise data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximises parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie (J. Phys. Chem, Vol. 81, p. 2340-2361, 1977). In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system’s size

STOCHSIMGPU Parallel stochastic simulation for the Systems\ud Biology Toolbox 2 for MATLAB

Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which exploits graphics processing units (GPUs)for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB.\ud \ud Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM), and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user’s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2

ICONGETM v1.0 – flexible NUOPC-driven two-way coupling via ESMF exchange grids between the unstructured-grid atmosphere model ICON and the structured-grid coastal ocean model GETM

Two-way model coupling is important for representing the mutual interactions and feedbacks between atmosphere and ocean dynamics. This work presents the development of the two-way coupled model system ICONGETM, consisting of the atmosphere model ICON and the ocean model GETM. ICONGETM is built on the latest NUOPC coupling software with flexible data exchange and conservative interpolation via ESMF exchange grids. With ICON providing a state-of-the-art kernel for numerical weather prediction on an unstructured mesh and GETM being an established coastal ocean model, ICONGETM is especially suited for high-resolution studies. For demonstration purposes the newly developed model system has been applied to a coastal upwelling scenario in the central Baltic Sea

Numerical issues of the Total Exchange Flow (TEF) analysis framework for quantifying estuarine circulation

For more than a century, estuarine exchange flow has been quantified by means of the Knudsen relations which connect bulk quantities such as inflow and outflow volume fluxes and salinities. These relations are closely linked to estuarine mixing. The recently developed Total Exchange Flow (TEF) analysis framework, which uses salinity coordinates to calculate these bulk quantities, allows an exact formulation of the Knudsen relations in realistic cases. There are however numerical issues, since the original method does not converge to the TEF bulk values for an increasing number of salinity classes. In the present study, this problem is investigated and the method of dividing salinities, described by MacCready et al. (2018), is mathematically introduced. A challenging yet compact analytical scenario for a well-mixed estuarine exchange flow is investigated for both methods, showing the proper convergence of the dividing salinity method. Furthermore, the dividing salinity method is applied to model results of the Baltic Sea to demonstrate the analysis of realistic exchange flows and exchange flows with more than two layers.</p

Interactive impacts of meteorological and hydrological conditions on the physical and biogeochemical structure of a coastal system

The German Bight was exposed to record high riverine discharges in June 2013, as a result of flooding of the Elbe and Weser rivers. Several anomalous observations suggested that the hydrodynamical and biogeochemical states of the system were impacted by this event. In this study, we developed a biogeochemical model and coupled it with a previously introduced high-resolution hydrodynamical model of the southern North Sea in order to better characterize these impacts and gain insight into the underlying processes. Performance of the model was assessed using an extensive set of in situ measurements for the period 2011–2014. We first improved the realism of the hydrodynamic model with regard to the representation of cross-shore gradients, mainly through inclusion of flow-dependent horizontal mixing. Among other characteristic features of the system, the coupled model system can reproduce the low salinities, high nutrient concentrations and low oxygen concentrations in the bottom layers observed within the German Bight following the flood event. Through a scenario analysis, we examined the sensitivity of the patterns observed during July 2013 to the hydrological and meteorological forcing in isolation. Within the region of freshwater influence (ROFI) of the Elbe–Weser rivers, the flood event clearly dominated the changes in salinity and nutrient concentrations, as expected. However, our findings point to the relevance of the peculiarities in the meteorological conditions in 2013 as well: a combination of low wind speeds, warm air temperatures and cold bottom-water temperatures resulted in a strong thermal stratification in the outer regions and limited vertical nutrient transport to the surface layers. Within the central region, the thermal and haline dynamics interactively resulted in an intense density stratification. This intense stratification, in turn, led to enhanced primary production within the central region enriched by nutrients due to the flood but led to reduction within the nutrient-limited outer region, and it caused a widespread oxygen depletion in bottom waters. Our results further point to the enhancement of the current velocities at the surface as a result of haline stratification and to intensification of the thermohaline estuarine-like circulation in the Wadden Sea, both driven by the flood event