Parallel implementation of the SHYFEM (System of HydrodYnamic Finite Element Modules) model

This paper presents the message passing interface (MPI)-based parallelization of the three-dimensional hydrodynamic model SHYFEM (System of HydrodYnamic Finite Element Modules). The original sequential version of the code was parallelized in order to reduce the execution time of high-resolution configurations using state-of-the-art high-performance computing (HPC) systems. A distributed memory approach was used, based on the MPI. Optimized numerical libraries were used to partition the unstructured grid (with a focus on load balancing) and to solve the sparse linear system of equations in parallel in the case of semi-to-fully implicit time stepping. The parallel implementation of the model was validated by comparing the outputs with those obtained from the sequential version. The performance assessment demonstrates a good level of scalability with a realistic configuration used as benchmark

Scalable Fast Multipole Methods on Heterogeneous Architecture

The N-body problem appears in many computational physics simulations. At each time step the computation involves an all-pairs sum whose complexity is quadratic, followed by an update of particle positions. This cost means that it is not practical to solve such dynamic N-body problems on large scale. To improve this situation, we use both algorithmic and hardware approaches. Our algorithmic approach is to use the Fast Multipole Method (FMM), which is a divide-and-conquer algorithm that performs a fast N-body sum using a spatial decomposition and is often used in a time-stepping or iterative loop, to reduce such quadratic complexity to linear with guaranteed accuracy. Our hardware approach is to use heterogeneous clusters, which comprised of nodes that contain multi-core CPUs tightly coupled with accelerators, such as graphics processors unit (GPU) as our underline parallel processing hardware, on which efficient implementations require highly non-trivial re-designed algorithms. In this dissertation, we fundamentally reconsider the FMM algorithms on heterogeneous architectures to achieve a significant improvement over recent/previous implementations in literature and to make the algorithm ready for use as a workhorse simulation tool for both time-dependent vortex flow problems and for boundary element methods. Our major contributions include: 1. Novel FMM data structures using parallel construction algorithms for dynamic problems. 2. A fast hetegenenous FMM algorithm for both single and multiple computing nodes. 3. An efficient inter-node communication management using fast parallel data structures. 4. A scalable FMM algorithm using novel Helmholz decomposition for Vortex Methods (VM). The proposed algorithms can handle non-uniform distributions with irregular partition shapes to achieve workload balance and their MPI-CUDA implementations are highly tuned up and demonstrate the state of the art performances

Computational Methods in Science and Engineering : Proceedings of the Workshop SimLabs@KIT, November 29 - 30, 2010, Karlsruhe, Germany

In this proceedings volume we provide a compilation of article contributions equally covering applications from different research fields and ranging from capacity up to capability computing. Besides classical computing aspects such as parallelization, the focus of these proceedings is on multi-scale approaches and methods for tackling algorithm and data complexity. Also practical aspects regarding the usage of the HPC infrastructure and available tools and software at the SCC are presented

A comprehensive survey of recent advancements in molecular communication

With much advancement in the field of nanotechnology, bioengineering and synthetic biology over the past decade, microscales and nanoscales devices are becoming a reality. Yet the problem of engineering a reliable communication system between tiny devices is still an open problem. At the same time, despite the prevalence of radio communication, there are still areas where traditional electromagnetic waves find it difficult or expensive to reach. Points of interest in industry, cities, and medical applications often lie in embedded and entrenched areas, accessible only by ventricles at scales too small for conventional radio waves and microwaves, or they are located in such a way that directional high frequency systems are ineffective. Inspired by nature, one solution to these problems is molecular communication (MC), where chemical signals are used to transfer information. Although biologists have studied MC for decades, it has only been researched for roughly 10 year from a communication engineering lens. Significant number of papers have been published to date, but owing to the need for interdisciplinary work, much of the results are preliminary. In this paper, the recent advancements in the field of MC engineering are highlighted. First, the biological, chemical, and physical processes used by an MC system are discussed. This includes different components of the MC transmitter and receiver, as well as the propagation and transport mechanisms. Then, a comprehensive survey of some of the recent works on MC through a communication engineering lens is provided. The paper ends with a technology readiness analysis of MC and future research directions

On the tree-root-soil-continuum - temporal and spatial coupling of the belowground carbon flux

The direct flux of current assimilates from the tree canopy to the belowground compartment drives roughly half of the soil respiratory activity in boreal forests. This thesis focuses on temporal and spatial aspects of the carbon (C) flux within the tree-root-soil continuum in temperate and boreal forests. I used the stable isotopes 13C and 15N to follow C from the canopy to the belowground compartment and the flow of nitrogen in the reverse direction. The C isotope composition of photosynthate varies diurnally, but such variations could not be observed in soil-respired CO2. Labelling of small (up to 4.5 m) Pinus sylvestris trees with 13CO2 showed that it took two days for the photosynthate to reach the soil. The velocity of the phloem flux was c. 0.1 m h-1. This flux of C is absolutely vital for the production of sporocarps by ectomycorrhizal fungi, as shown by their paucity in plots with girdled trees. It is also likely to be important for other soil microorganisms; addition of a labile 13C labelled C source revealed a lack of labile C substrates in girdled plots. The reduction in the abundance of ectomycorrhizal sporocarps from the edges to the centre of girdled plots and a 15N uptake experiment showed that lateral spread of ectomycorrhizal roots was on average 4 to 5 m from the trunks. Thus, it can be expected that an area of c. 60 m2 of soil is under the influence of direct flux of current assimilates from the tree canopy of a single tree. Areas of influence of several trees overlapped. I conclude that canopy and soil processes are coupled with time lags of a few days. The direct impact of plant photosynthate should be considered more often in studies of soil. The 13CO2 labelling study demonstrated that it is now possible to follow at a very high resolution the fate of this C into the belowground system

Consortium for materials development in space

The status of the Consortium for Materials Development in Space (CMDS) is reviewed. Individual projects are outlined and the status of Get Away Special (GAS) 105 is summarized