Mixing multi-core CPUs and GPUs for scientific simulation software

Recent technological and economic developments have led to widespread availability of multi-core CPUs and specialist accelerator processors such as graphical processing units (GPUs). The accelerated computational performance possible from these devices can be very high for some applications paradigms. Software languages and systems such as NVIDIA's CUDA and Khronos consortium's open compute language (OpenCL) support a number of individual parallel application programming paradigms. To scale up the performance of some complex systems simulations, a hybrid of multi-core CPUs for coarse-grained parallelism and very many core GPUs for data parallelism is necessary. We describe our use of hybrid applica- tions using threading approaches and multi-core CPUs to control independent GPU devices. We present speed-up data and discuss multi-threading software issues for the applications level programmer and o er some suggested areas for language development and integration between coarse-grained and ne-grained multi-thread systems. We discuss results from three common simulation algorithmic areas including: partial di erential equations; graph cluster metric calculations and random number generation. We report on programming experiences and selected performance for these algorithms on: single and multiple GPUs; multi-core CPUs; a CellBE; and using OpenCL. We discuss programmer usability issues and the outlook and trends in multi-core programming for scienti c applications developers

Simulation modelling and visualisation: toolkits for building artificial worlds

Simulations users at all levels make heavy use of compute resources to drive computational simulations for greatly varying applications areas of research using different simulation paradigms. Simulations are implemented in many software forms, ranging from highly standardised and general models that run in proprietary software packages to ad hoc hand-crafted simulations codes for very specific applications. Visualisation of the workings or results of a simulation is another highly valuable capability for simulation developers and practitioners. There are many different software libraries and methods available for creating a visualisation layer for simulations, and it is often a difficult and time-consuming process to assemble a toolkit of these libraries and other resources that best suits a particular simulation model. We present here a break-down of the main simulation paradigms, and discuss differing toolkits and approaches that different researchers have taken to tackle coupled simulation and visualisation in each paradigm

Effects of oil and natural or synthetic vitamin E on ruminal and milk fatty acid profiles in cows receiving a high-starch diet

Among trans fatty acids, trans-10,cis-12 CLA has negative effects on cow milk fat production and can affect human health. In high-yielding dairy cows, a shift from the trans-11 to the trans-10 pathway of biohydrogenation (BH) can occur in the rumen of cows receiving high-concentrate diets, especially when the diet is supplemented with unsaturated fat sources. In some but not all experiments, vitamin E has been shown to control this shift. To ascertain the effects of vitamin E on this shift of BH pathway, 2 studies were conducted. The first study explored in vitro the effects of addition of natural (RRR-α-tocopherol acetate) and synthetic (dl-α-tocopherol acetate) vitamin E. Compared with control and synthetic vitamin E, the natural form resulted in a greater trans-10/trans-11 ratio; however, the effect was very low, suggesting that vitamin E was neither a limiting factor for rumen BH nor a modulator of the BH pathway. An in vivo study investigated the effect of natural vitamin E (RRR-α-tocopherol) on this shift and subsequent milk fat depression. Six rumenfistulated lactating Holstein cows were assigned to a 2 × 2 crossover design. Cows received 20-kg DM of a control diet based on corn silage with 22% of wheat, and after 2 wk of adaptation, the diet was supplemented with 600 g of sunflower oil for 2 more weeks. During the last week of this 4-wk experimental period, cows were divided into 2 groups: an unsupplemented control group and a group receiving 11 g of RRR-α-tocopherol acetate per day. A trans-10 shift of ruminal BH associated with milk fat depression due to oil supplementation of a high-wheat diet was observed, but vitamin E supplementation of dairy cows did not result in a reversal toward a trans-11 BH pathway, and did not restore milk fat content

A Block-Based Union-Find Algorithm to Label Connected Components on GPUs

In this paper, we introduce a novel GPU-based Connected Components Labeling algorithm: the Block-based Union Find. The proposed strategy significantly improves an existing GPU algorithm, taking advantage of a block-based approach. Experimental results on real cases and synthetically generated datasets demonstrate the superiority of the new proposal with respect to state-of-the-art

Galacto-Oligosaccharides : production, properties, applications, and significance as prebiotics

Galacto-oligosaccharides (GOS) have now been definitely established as prebiotic ingredients after in vitro and animal and human in vivo studies. Currently, GOS are produced by glycoside hydrolases (GH) using lactose as substrate. Converting lactose into GOS by GH results in mixtures containing GOS of different degrees of polymerization (DP), unreacted lactose, and monomeric sugars (glucose and galactose). Recent and future developments in the production of GOS aim at delivering purer and more efficient mixtures. To produce high-GOS-content mixtures, GH should not only have good ability to catalyze the transgalactosylation reaction relative to hydrolysis, but also have low affinity for the GOS formed relative to the affinity for lactose. In this article, several microbial GH, proposed for the synthesis of GOS, are hierarchized according to the referred performance indicators. In addition, strategies for process improvement are discussed. Besides the differences in purity of GOS mixtures, differences in the position of the glycosidic linkages occur, because different enzymes have different regiochemical selectivity. Depending on oligosaccharide composition, GOS products will vary in terms of prebiotic activity, as well as other physiological effects. This review focuses on GOS production from synthesis to purification processes. Physicochemical characteristics, physiological effects, and applications of these prebiotic ingredients are summarized. Regulatory aspects of GOS-containing food products are also highlighted with emphasis on the current process of health claims evaluation in Europe.Agência da Inovação-Progama IDEIA (Portugal)Fundação para a Ciência e a Tecnologia (FCT

An overview of the recent developments on fructooligosaccharide production and applications

Over the past years, many researchers have suggested that deficiencies in the diet can lead to disease states and that some diseases can be avoided through an adequate intake of relevant dietary components. Recently, a great interest in dietary modulation of the human gut has been registered. Prebiotics, such as fructooligosaccharides (FOS), play a key role in the improvement of gut microbiota balance and in individual health. FOS are generally used as components of functional foods, are generally regarded as safe (generally recognized as safe status—from the Food and Drug Administration, USA), and worth about 150€ per kilogram. Due to their nutrition- and health-relevant properties, such as moderate sweetness, low carcinogenicity, low calorimetric value, and low glycemic index, FOS have been increasingly used by the food industry. Conventionally, FOS are produced through a two-stage process that requires an enzyme production and purification step in order to proceed with the chemical reaction itself. Several studies have been conducted on the production of FOS, aiming its optimization toward the development of more efficient production processes and their potential as food ingredients. The improvement of FOS yield and productivity can be achieved by the use of different fermentative methods and different microbial sources of FOS producing enzymes and the optimization of nutritional and culture parameter; therefore, this review focuses on the latest progresses in FOS research such as its production, functional properties, and market data.Agencia de Inovacao (AdI)-Project BIOLIFE reference PRIME 03/347. Ana Dominguez acknowledges Fundacao para a Ciencia e a Tecnologia, Portugal, for her PhD grant reference SFRH/BD/23083/2005